3CDX

Crystal structure of succinylglutamatedesuccinylase/aspartoacylase from Rhodobacter sphaeroides

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	294	200mM Calcium acetate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 152.475	α = 90
b = 174.426	β = 90
c = 77.406	γ = 90

Symmetry
Space Group	P 21 21 2

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	MAR CCD 165 mm		2007-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	22.81	95.3	0.114	0.114	11.7	5.4	115134	115134			27.9

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)
	2.1	2.21	86.3		0.519	0.519	2.9	5.1	15035

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.1	20	115013	115013	5818	95.22	0.184	0.181	0.244	RANDOM	36.112

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]
-1.3			1.63		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.423
r_dihedral_angle_4_deg	17.775
r_dihedral_angle_3_deg	13.314
r_dihedral_angle_1_deg	6.924
r_scangle_it	3.147
r_scbond_it	2.097
r_angle_refined_deg	1.484
r_mcangle_it	1.31
r_mcbond_it	0.834
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.423
r_dihedral_angle_4_deg	17.775
r_dihedral_angle_3_deg	13.314
r_dihedral_angle_1_deg	6.924
r_scangle_it	3.147
r_scbond_it	2.097
r_angle_refined_deg	1.484
r_mcangle_it	1.31
r_mcbond_it	0.834
r_nbtor_refined	0.304
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.193
r_symmetry_hbond_refined	0.171
r_xyhbond_nbd_refined	0.151
r_metal_ion_refined	0.123
r_chiral_restr	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14894
Nucleic Acid Atoms
Solvent Atoms	1256
Heterogen Atoms	6

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

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.