2VD9 | pdb_00002vd9

The crystal structure of alanine racemase from Bacillus anthracis (BA0252) with bound L-Ala-P

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VD8	PDB ENTRY 2VD8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		25% (W/V) POLYETHYLENE GLYCOL 3350, 0.1M BIS-TRIS PH6.5, SOAKED IN 10MM L-ALA-P FOR 45 MINUTES, CRYOPROTECTED IN 25% GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
2.28	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.692	α = 90
b = 96.504	β = 90
c = 140.66	γ = 90

Symmetry
Space Group	P 21 21 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	MARRESEARCH		2007-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	2.1	50	99.9	0.23	7.1	6.9		48124

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	2.1	2.18	9		0.88	1.2	4.1

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2VD8	2.1	45.64	45596	2434	99.7	0.19	0.188	0.19	0.239	0.24	RANDOM	14.3

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]
0.03			-0.05		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.064
r_dihedral_angle_4_deg	12.771
r_dihedral_angle_3_deg	11.569
r_dihedral_angle_1_deg	6.288
r_angle_refined_deg	1.195
r_mcangle_it	0.914
r_angle_other_deg	0.912
r_scangle_it	0.859
r_mcbond_it	0.769
r_scbond_it	0.535
r_symmetry_vdw_other	0.231
r_symmetry_vdw_refined	0.224
r_nbd_other	0.195
r_symmetry_hbond_refined	0.193
r_nbd_refined	0.189
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.153
r_nbtor_other	0.084
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6196
Nucleic Acid Atoms
Solvent Atoms	871
Heterogen Atoms	94

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing