2VD8

The crystal structure of alanine racemase from Bacillus anthracis (BA0252)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SFT	PDB ENTRY 1SFT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		25% (W/V) POLYETHYLENE GLYCOL 3350, 0.1 M BIS-TRIS PH 6.5

Crystal Properties
Matthews coefficient	Solvent content
1.99	38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.552	α = 90
b = 88.365	β = 90
c = 138.968	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	1.47	50	96.3	0.11	18.6	9.9		116056

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	1.47	1.52	78.3		0.95	1.2	4.6

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 1SFT	1.47	44.19	110132	5826	96.2	0.169	0.168	0.17	0.199	0.21	RANDOM	10.33

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.263
r_dihedral_angle_4_deg	11.453
r_dihedral_angle_3_deg	10.772
r_dihedral_angle_1_deg	6.257
r_scangle_it	3.038
r_mcangle_it	2.201
r_scbond_it	1.987
r_mcbond_it	1.826
r_angle_refined_deg	1.412
r_angle_other_deg	1.024
r_symmetry_vdw_refined	0.238
r_chiral_restr	0.219
r_symmetry_vdw_other	0.217
r_nbd_refined	0.215
r_nbd_other	0.202
r_nbtor_refined	0.181
r_symmetry_hbond_refined	0.165
r_xyhbond_nbd_refined	0.151
r_nbtor_other	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
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	6205
Nucleic Acid Atoms
Solvent Atoms	1020
Heterogen Atoms	37

Software

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