4WJI

Crystal structure of cyclohexadienyl dehydrogenase from Sinorhizobium meliloti in complex with NADP and tyrosine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	0.2 ul of 11 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azid, 0.5 mM TCEP, 7mM NADP and 20 mM tyrosine were mixed with 0.2 ul of the Index condition #83 (0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.409	α = 90
b = 68.891	β = 94.34
c = 51.097	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Beryllium Lenses	2013-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.4	50	95.6	0.066	0.084	0.052	14.3	2.3		49774		-3	11.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42	93.4		0.369	0.501	0.336	0.734	1.8	1.7	2421

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.4	50	49707	2524	95.6	0.1173	0.1151	0.1587	RANDOM	15.987

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.64		-1.2	-0.19		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.792
r_sphericity_free	20.153
r_dihedral_angle_4_deg	14.731
r_dihedral_angle_3_deg	12.019
r_sphericity_bonded	11.494
r_dihedral_angle_1_deg	4.853
r_rigid_bond_restr	4.816
r_mcangle_it	2.219
r_mcbond_it	1.802
r_mcbond_other	1.801

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.792
r_sphericity_free	20.153
r_dihedral_angle_4_deg	14.731
r_dihedral_angle_3_deg	12.019
r_sphericity_bonded	11.494
r_dihedral_angle_1_deg	4.853
r_rigid_bond_restr	4.816
r_mcangle_it	2.219
r_mcbond_it	1.802
r_mcbond_other	1.801
r_angle_other_deg	1.634
r_angle_refined_deg	1.616
r_chiral_restr	0.108
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2162
Nucleic Acid Atoms
Solvent Atoms	276
Heterogen Atoms	66

Software

Software
Software Name	Purpose
Blu-Ice	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.