6YVL

Human OMPD-domain of UMPS in complex with the substrate OMP at 1.25 Angstroms resolution, 1.42 MGy exposure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QCD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Crystallization: 100 mM Tris/HCl pH 8.0, 1.9 - 2.1 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol Soaking: 100 mM Tris/HCl pH 8.0, 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 50 mM OMP Cryo-protection: 100 mM Tris/HCl pH 8.0, 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 50 mM OMP
Crystal Properties
Matthews coefficientSolvent content
2.4750.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.31α = 90
b = 116.85β = 90
c = 61.97γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.82660PETRA III, EMBL c/o DESYP14 (MX2)

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
11.2519.6899.80.080.087115.746.8187754017.875
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.251.399.91.3821.4960.6621.696.837

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2QCD1.2519.6873773376799.780.13020.12880.1576RANDOM15.226
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]
0.82-0.42-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.147
r_dihedral_angle_4_deg16.691
r_dihedral_angle_3_deg12.509
r_rigid_bond_restr9.253
r_dihedral_angle_1_deg6.699
r_angle_other_deg2.263
r_angle_refined_deg1.461
r_chiral_restr0.084
r_bond_other_d0.035
r_gen_planes_other0.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.147
r_dihedral_angle_4_deg16.691
r_dihedral_angle_3_deg12.509
r_rigid_bond_restr9.253
r_dihedral_angle_1_deg6.699
r_angle_other_deg2.263
r_angle_refined_deg1.461
r_chiral_restr0.084
r_bond_other_d0.035
r_gen_planes_other0.014
r_gen_planes_refined0.012
r_bond_refined_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1962
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms36

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction