2JFQ | pdb_00002jfq

Crystal structure of Staphylococcus aureus glutamate racemase in complex with D- Glutamate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JFP	PDB ENTRY 2JFP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.4		PROTEIN FORMULATED AT 10 MG/ML WITH 200 MM AMMONIUM ACETATE PH 7.4, 5 MM D-L GLUTAMATE, 1 MM TCEP AND CRYSTALLISED WITH 0.17 MM AMMONIUM SULPHATE AND 25% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
3	59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.43	α = 90
b = 88.87	β = 109
c = 96.56	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	MARRESEARCH		2002-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711		MAX II	I711

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	2.13	34	98.2	0.1	6.7	4		41628		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	2.13	2.22	90.7		0.34	2.2	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2JFP	2.15	34	41628	2103		0.202	0.2012	0.229	RANDOM	27.04

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]
1.867		-1.673	-3.991		2.124

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_deg	1.19107
c_bond_d	0.005627
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4160
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	20

Software

Software
Software Name	Purpose
CNX	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing