6ZX0

OMPD-domain of human UMPS in complex with the substrate OMP at 1.25 Angstroms resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8293Crystallization: 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
2.4950.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.766α = 90
b = 116.906β = 90
c = 62.047γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.76530PETRA 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
11.158.521000.0710.0770.99913.536.73711438314.329
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)
11.11.151001.1091.2020.7291.896.792

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 REPLACEMENTTHROUGHOUT2QCD1.2558.5274471380299.970.11740.11640.1368RANDOM13.41
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]
0.79-0.35-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.144
r_dihedral_angle_4_deg17.486
r_dihedral_angle_3_deg12.162
r_rigid_bond_restr7.386
r_dihedral_angle_1_deg6.795
r_angle_other_deg2.26
r_angle_refined_deg1.455
r_chiral_restr0.08
r_bond_other_d0.035
r_gen_planes_other0.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.144
r_dihedral_angle_4_deg17.486
r_dihedral_angle_3_deg12.162
r_rigid_bond_restr7.386
r_dihedral_angle_1_deg6.795
r_angle_other_deg2.26
r_angle_refined_deg1.455
r_chiral_restr0.08
r_bond_other_d0.035
r_gen_planes_other0.014
r_gen_planes_refined0.011
r_bond_refined_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1962
Nucleic Acid Atoms
Solvent Atoms335
Heterogen Atoms26

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction