7OQM

Human OMPD-domain of UMPS in complex with substrate OMP at 1.05 Angstroms resolution, 20 minutes soaking


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8293.15Ammonium sulfate, Tris/HCl, Glutathion, Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.4750.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.964α = 90
b = 61.882β = 113.09
c = 70.052γ = 90
Symmetry
Space GroupP 1 21 1

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)0.827PETRA 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
11.0542.5197.20.050.0590.99912.353.49124870512.916
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)
11.051.0893.30.80.9630.6611.73.19

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 REPLACEMENTTHROUGHOUT6ZWY1.0542.512364441226497.310.12160.1210.1336RANDOM13.795
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]
0.180.57-0.970.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.966
r_dihedral_angle_4_deg16.092
r_dihedral_angle_3_deg12.904
r_dihedral_angle_1_deg6.73
r_angle_other_deg1.525
r_angle_refined_deg1.468
r_rigid_bond_restr0.884
r_chiral_restr0.08
r_gen_planes_refined0.008
r_bond_refined_d0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.966
r_dihedral_angle_4_deg16.092
r_dihedral_angle_3_deg12.904
r_dihedral_angle_1_deg6.73
r_angle_other_deg1.525
r_angle_refined_deg1.468
r_rigid_bond_restr0.884
r_chiral_restr0.08
r_gen_planes_refined0.008
r_bond_refined_d0.007
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3923
Nucleic Acid Atoms
Solvent Atoms712
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction