7NBD

Crystal structure of human serine racemase in complex with DSiP fragment Z235449082, 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
2.141.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.012α = 90
b = 154.846β = 98.043
c = 85.451γ = 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 I04-10.91578DiamondI04-1

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
11.8684.61940.0730.10.9988.93.59634037.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.861.97820.9120.471.13.5

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-VALUE6ZUJ1.86584.696297483093.910.1780.17620.207437.903
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]
-0.2450.2310.293-0.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.249
r_dihedral_angle_4_deg22.343
r_dihedral_angle_3_deg15.291
r_lrange_it11.187
r_dihedral_angle_1_deg6.162
r_scangle_it4.707
r_mcangle_it3.407
r_scbond_it3.189
r_mcbond_it2.279
r_angle_refined_deg1.669
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.249
r_dihedral_angle_4_deg22.343
r_dihedral_angle_3_deg15.291
r_lrange_it11.187
r_dihedral_angle_1_deg6.162
r_scangle_it4.707
r_mcangle_it3.407
r_scbond_it3.189
r_mcbond_it2.279
r_angle_refined_deg1.669
r_symmetry_xyhbond_nbd_refined0.326
r_nbtor_refined0.314
r_symmetry_nbd_refined0.264
r_nbd_refined0.253
r_xyhbond_nbd_refined0.239
r_metal_ion_refined0.171
r_symmetry_metal_ion_refined0.117
r_chiral_restr0.114
r_bond_refined_d0.01
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9472
Nucleic Acid Atoms
Solvent Atoms1053
Heterogen Atoms179

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing