6ZUJ

Human serine racemase holoenzyme from 20% DMSO soak (XChem crystallographic fragment screen).


X-RAY DIFFRACTION

Starting Model(s)

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

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
2.1141.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.062α = 90
b = 154.998β = 98.26
c = 85.652γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-07-13MSINGLE 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)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
11.884.76497.80.0680.0810.0430.9979.463.41111815
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8395.610.7040.8290.4360.6511.693.54

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-VALUE6SLH1.884.764111681550897.6390.1810.17890.219834.405
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]
0.0120.528-0.2470.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.181
r_dihedral_angle_4_deg21.498
r_dihedral_angle_3_deg14.485
r_lrange_it9.435
r_dihedral_angle_1_deg6.449
r_scangle_it2.579
r_mcangle_it2.325
r_scbond_it1.635
r_mcbond_it1.39
r_angle_refined_deg1.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.181
r_dihedral_angle_4_deg21.498
r_dihedral_angle_3_deg14.485
r_lrange_it9.435
r_dihedral_angle_1_deg6.449
r_scangle_it2.579
r_mcangle_it2.325
r_scbond_it1.635
r_mcbond_it1.39
r_angle_refined_deg1.319
r_nbtor_refined0.307
r_symmetry_nbd_refined0.284
r_nbd_refined0.233
r_symmetry_xyhbond_nbd_refined0.215
r_metal_ion_refined0.173
r_xyhbond_nbd_refined0.152
r_chiral_restr0.1
r_symmetry_metal_ion_refined0.04
r_gen_planes_refined0.007
r_bond_refined_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9412
Nucleic Acid Atoms
Solvent Atoms792
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing