7NBH

Crystal structure of human serine racemase in complex with DSiP fragment Z26781964, 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 = 48.18α = 90
b = 154.88β = 98.04
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)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
11.7751.697.10.0720.0980.9978.23.4116780
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)
11.771.8296.31.0480.30213.3

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-VALUE6ZUJ1.7747.752116737585997.0010.1710.16940.201835.476
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]
-0.3850.290.588-0.274
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.999
r_dihedral_angle_4_deg21.461
r_dihedral_angle_3_deg14.906
r_lrange_it10.565
r_dihedral_angle_1_deg6.755
r_scangle_it4.863
r_scbond_it3.446
r_mcangle_it3.332
r_mcbond_it2.343
r_angle_refined_deg1.734
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.999
r_dihedral_angle_4_deg21.461
r_dihedral_angle_3_deg14.906
r_lrange_it10.565
r_dihedral_angle_1_deg6.755
r_scangle_it4.863
r_scbond_it3.446
r_mcangle_it3.332
r_mcbond_it2.343
r_angle_refined_deg1.734
r_nbtor_refined0.31
r_symmetry_nbd_refined0.276
r_symmetry_xyhbond_nbd_refined0.227
r_nbd_refined0.221
r_metal_ion_refined0.192
r_xyhbond_nbd_refined0.175
r_chiral_restr0.116
r_bond_refined_d0.013
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9435
Nucleic Acid Atoms
Solvent Atoms975
Heterogen Atoms250

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing