3OUT | pdb_00003out

Crystal structure of glutamate racemase from Francisella tularensis subsp. tularensis SCHU S4 in complex with D-glutamate.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	295	25% PEG 3350, 0.1 M Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.06	α = 90
b = 98.06	β = 90
c = 154.15	γ = 90

Symmetry
Space Group	P 43 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	MIRROR	2010-08-13	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)	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	1.65	25.2	99.9	0.091	14.71	12.6	172747	172747		-3	24.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.65	1.68	99.8		0.499	3.16	11	9026

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.65	25.22	86104	86104	4544	99.87	0.16416	0.16265	0.1738	0.1927	0.2016	RANDOM	12.396

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]
-0.31			-0.31		0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.64
r_dihedral_angle_4_deg	21.185
r_dihedral_angle_3_deg	12.299
r_dihedral_angle_1_deg	5.812
r_scangle_it	4.425
r_scbond_it	2.902
r_mcangle_it	1.64
r_angle_refined_deg	1.537
r_angle_other_deg	0.986
r_mcbond_it	0.923

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.64
r_dihedral_angle_4_deg	21.185
r_dihedral_angle_3_deg	12.299
r_dihedral_angle_1_deg	5.812
r_scangle_it	4.425
r_scbond_it	2.902
r_mcangle_it	1.64
r_angle_refined_deg	1.537
r_angle_other_deg	0.986
r_mcbond_it	0.923
r_mcbond_other	0.271
r_chiral_restr	0.094
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6168
Nucleic Acid Atoms
Solvent Atoms	601
Heterogen Atoms	30

Software

Software
Software Name	Purpose
Blu-Ice	data collection
CCP4	model building
MrBUMP	phasing
PHENIX	model building
REFMAC	refinement
XSCALE	data scaling
CCP4	phasing
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.