3OO2

2.37 Angstrom resolution crystal structure of an alanine racemase (alr) from Staphylococcus aureus subsp. aureus COL

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	295	7.6 mg/mL protein in 10 mM Tris/HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Crystals grew from 0.1 M MIB buffer pH 5.0, 25 % (w/v) PEG1500 (The PACT suite condition #14), VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.735	α = 90
b = 118.31	β = 90
c = 129.008	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	MARMOSAIC 225 mm CCD	Be-Lenses/Diamond Laue Mono	2010-08-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.37	30	99.6	0.077	18.36	4.9	30323	30323		-3

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)
	2.37	2.41	100		0.572	2.66	4.9	1494

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	Balbes model	2.37	29.59	28741	28741	1533	99.52	0.20259	0.19972	0.25683	RANDOM	53.394

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]
1.52			-1.62		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.905
r_dihedral_angle_4_deg	14.623
r_dihedral_angle_3_deg	11.545
r_scangle_it	4.85
r_scbond_it	3.317
r_dihedral_angle_1_deg	3.007
r_mcangle_it	1.949
r_angle_refined_deg	1.567
r_mcbond_it	1.105
r_angle_other_deg	0.835

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.905
r_dihedral_angle_4_deg	14.623
r_dihedral_angle_3_deg	11.545
r_scangle_it	4.85
r_scbond_it	3.317
r_dihedral_angle_1_deg	3.007
r_mcangle_it	1.949
r_angle_refined_deg	1.567
r_mcbond_it	1.105
r_angle_other_deg	0.835
r_mcbond_other	0.299
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5866
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	24

Software

Software
Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

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.