7NBC

Crystal structure of human serine racemase in complex with DSiP fragment Z2856434779, 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 = 48.15α = 90
b = 154.86β = 98.08
c = 85.48γ = 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)Rpim 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
11.7177.698.20.0670.0930.9978.33.4130785
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)
11.711.7497.20.9480.30512.9

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-VALUE6ZUJ1.7177.4130740652798.0940.1760.17440.201532.375
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]
-0.3610.2250.417-0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.742
r_dihedral_angle_4_deg20.903
r_dihedral_angle_3_deg14.537
r_lrange_it9.728
r_dihedral_angle_1_deg6.459
r_scangle_it3.003
r_mcangle_it2.493
r_scbond_it1.924
r_mcbond_it1.483
r_angle_refined_deg1.356
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.742
r_dihedral_angle_4_deg20.903
r_dihedral_angle_3_deg14.537
r_lrange_it9.728
r_dihedral_angle_1_deg6.459
r_scangle_it3.003
r_mcangle_it2.493
r_scbond_it1.924
r_mcbond_it1.483
r_angle_refined_deg1.356
r_nbtor_refined0.311
r_symmetry_xyhbond_nbd_refined0.239
r_symmetry_nbd_refined0.223
r_nbd_refined0.216
r_metal_ion_refined0.165
r_xyhbond_nbd_refined0.147
r_chiral_restr0.099
r_bond_refined_d0.007
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9507
Nucleic Acid Atoms
Solvent Atoms867
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing