3L6C

X-ray crystal structure of rat serine racemase in complex with malonate a potent inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		HUMAN SERINE RACEMASE SOLVED BY SELENOMETHIONINE SAD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.593	α = 90
b = 110.593	β = 90
c = 47.917	γ = 120

Symmetry
Space Group	P 3

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		2008-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.54187

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.2	55.29	97.7	0.06	0.06	9.4	2.5	30389	30389	2	3	38.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.33	83.4		0.311	0.311	2.1	1.55	30389

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	HUMAN SERINE RACEMASE SOLVED BY SELENOMETHIONINE SAD	2.2	47.89	2	1.5	30389	30285	1586	95.9	0.219	0.219	0.216	0.267	RANDOM	47.64

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]
-0.04	-0.02		-0.04		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.731
r_dihedral_angle_4_deg	17.842
r_dihedral_angle_3_deg	17.685
r_dihedral_angle_1_deg	6.844
r_scangle_it	3.071
r_scbond_it	1.983
r_angle_refined_deg	1.604
r_mcangle_it	1.417
r_mcbond_it	0.806
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.731
r_dihedral_angle_4_deg	17.842
r_dihedral_angle_3_deg	17.685
r_dihedral_angle_1_deg	6.844
r_scangle_it	3.071
r_scbond_it	1.983
r_angle_refined_deg	1.604
r_mcangle_it	1.417
r_mcbond_it	0.806
r_nbtor_refined	0.3
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.214
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.097
r_symmetry_hbond_refined	0.064
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4779
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	46

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

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.