Experiment: 3JY9

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	298	2.1 - 1.5 D-L malic acid, pH 7.0, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.103	α = 90
b = 101.257	β = 90
c = 68.488	γ = 90

Symmetry
Space Group	C 2 2 21

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	ADSC QUANTUM 315		2005-12-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.00	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.1	47.55	94.7	0.054	0.061	12.2	3.7	19678	18628	0.1	0.1	29.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	86.1		0.24	0.305	2.5	2.05	1671

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	previous determined liganded structure	2.1	20	20050	18581	1469	94.56	0.201	0.201	0.195	0.271	RANDOM	28.953

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]
-0.44			0.28		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.892
r_dihedral_angle_4_deg	19.624
r_dihedral_angle_3_deg	17.312
r_dihedral_angle_1_deg	6.345
r_scangle_it	5.635
r_scbond_it	3.515
r_mcangle_it	2.248
r_angle_refined_deg	1.901
r_mcbond_it	1.232
r_chiral_restr	0.253

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.892
r_dihedral_angle_4_deg	19.624
r_dihedral_angle_3_deg	17.312
r_dihedral_angle_1_deg	6.345
r_scangle_it	5.635
r_scbond_it	3.515
r_mcangle_it	2.248
r_angle_refined_deg	1.901
r_mcbond_it	1.232
r_chiral_restr	0.253
r_bond_refined_d	0.023
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2363
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	27

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
d*TREK	data reduction
REFMAC	phasing

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.