7NBF

Crystal structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6ZUJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.2293100 mM MES pH 6.2 100 mM calcium chloride 5% ethylene glycol 20% PEG Smear Broad
Crystal Properties
Matthews coefficientSolvent content
2.1141.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.112α = 90
b = 154.937β = 97.957
c = 85.539γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.59984.71697.60.0590.0820.9978.93.315895629
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.5991.6393.40.6580.8890.3831.12.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6ZUJ1.684.7158845796297.4680.1730.17220.198228.988
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]
-0.110.1120.195-0.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.046
r_dihedral_angle_4_deg24.948
r_dihedral_angle_3_deg14.963
r_lrange_it10.177
r_dihedral_angle_1_deg6.233
r_scangle_it4.302
r_mcangle_it3.109
r_scbond_it2.879
r_mcbond_it2.002
r_angle_refined_deg1.882
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.046
r_dihedral_angle_4_deg24.948
r_dihedral_angle_3_deg14.963
r_lrange_it10.177
r_dihedral_angle_1_deg6.233
r_scangle_it4.302
r_mcangle_it3.109
r_scbond_it2.879
r_mcbond_it2.002
r_angle_refined_deg1.882
r_nbtor_refined0.317
r_symmetry_xyhbond_nbd_refined0.313
r_nbd_refined0.222
r_symmetry_nbd_refined0.203
r_xyhbond_nbd_refined0.189
r_metal_ion_refined0.168
r_chiral_restr0.127
r_symmetry_metal_ion_refined0.056
r_bond_refined_d0.013
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9445
Nucleic Acid Atoms
Solvent Atoms920
Heterogen Atoms218

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing