4Y2W

Crystal structure of a thermostable alanine racemase from Thermoanaerobacter tengcongensis MB4

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	289	22% PEG 4000, 0.1M Bis-Tris pH7.0

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.843	α = 90
b = 73.077	β = 90
c = 218.746	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	IMAGE PLATE	RIGAKU RAXIS IV++		2014-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	2.7	50	96.6	0.073	7.3	5.2		26832

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	2.7	2.75	83.4		0.261	2.7	3.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1SFT	2.7	50	25425	1353	96.38	0.2155	0.2136	0.2524	RANDOM	45.735

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]
-2.73			-0.06		2.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.796
r_dihedral_angle_4_deg	16.63
r_dihedral_angle_3_deg	14.095
r_dihedral_angle_1_deg	5.378
r_mcangle_it	1.859
r_mcbond_it	1.057
r_mcbond_other	1.057
r_angle_refined_deg	0.986
r_angle_other_deg	0.66
r_chiral_restr	0.051

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.796
r_dihedral_angle_4_deg	16.63
r_dihedral_angle_3_deg	14.095
r_dihedral_angle_1_deg	5.378
r_mcangle_it	1.859
r_mcbond_it	1.057
r_mcbond_other	1.057
r_angle_refined_deg	0.986
r_angle_other_deg	0.66
r_chiral_restr	0.051
r_bond_refined_d	0.004
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6212
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	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 R01GM133198.