7NBG

Crystal structure of human serine racemase in complex with DSiP fragment Z52314092, 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
2.0941.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.11α = 90
b = 154.76β = 98.14
c = 85.4γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-07-15MSINGLE 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
11.5377.495.90.0520.0750.99893.2177718
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)
11.531.57870.8040.4532.6

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-VALUE6ZUJ1.5377.38177667870695.8290.1830.18230.20228.092
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]
-0.0390.601-0.4610.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.717
r_dihedral_angle_4_deg18.352
r_dihedral_angle_3_deg13.136
r_lrange_it8.238
r_dihedral_angle_1_deg6.075
r_scangle_it1.946
r_mcangle_it1.699
r_scbond_it1.22
r_angle_refined_deg1.151
r_mcbond_it0.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.717
r_dihedral_angle_4_deg18.352
r_dihedral_angle_3_deg13.136
r_lrange_it8.238
r_dihedral_angle_1_deg6.075
r_scangle_it1.946
r_mcangle_it1.699
r_scbond_it1.22
r_angle_refined_deg1.151
r_mcbond_it0.99
r_nbtor_refined0.307
r_symmetry_xyhbond_nbd_refined0.255
r_symmetry_nbd_refined0.241
r_nbd_refined0.214
r_metal_ion_refined0.177
r_xyhbond_nbd_refined0.144
r_chiral_restr0.087
r_symmetry_metal_ion_refined0.063
r_gen_planes_refined0.005
r_bond_refined_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9368
Nucleic Acid Atoms
Solvent Atoms941
Heterogen Atoms159

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing