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)
TypeSourceAccession CodeDetails
experimental modelOtherHUMAN SERINE RACEMASE SOLVED BY SELENOMETHIONINE SAD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8295pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3146.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.593α = 90
b = 110.593β = 90
c = 47.917γ = 120
Symmetry
Space GroupP 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.54187

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.255.2997.70.060.069.42.530389303892338.2
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)RedundancyNumber Unique Reflections (All)
2.22.3383.40.3110.3112.11.5530389

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTHUMAN SERINE RACEMASE SOLVED BY SELENOMETHIONINE SAD2.247.8921.53038930285158695.90.2190.2190.2160.267RANDOM47.64
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]
-0.04-0.02-0.040.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.731
r_dihedral_angle_4_deg17.842
r_dihedral_angle_3_deg17.685
r_dihedral_angle_1_deg6.844
r_scangle_it3.071
r_scbond_it1.983
r_angle_refined_deg1.604
r_mcangle_it1.417
r_mcbond_it0.806
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.731
r_dihedral_angle_4_deg17.842
r_dihedral_angle_3_deg17.685
r_dihedral_angle_1_deg6.844
r_scangle_it3.071
r_scbond_it1.983
r_angle_refined_deg1.604
r_mcangle_it1.417
r_mcbond_it0.806
r_nbtor_refined0.3
r_symmetry_vdw_refined0.221
r_nbd_refined0.214
r_xyhbond_nbd_refined0.162
r_chiral_restr0.097
r_symmetry_hbond_refined0.064
r_bond_refined_d0.015
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4779
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms46

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling