6YWT

Human OMPD-domain of UMPS (K314AcK) in complex with 6-hydroxy-UMP at 1.05 Angstroms resolution


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 7.8, 1.6 - 1.8 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 5mg/mL OMPD, 12 mM BMP Cryo-protection: 100 mM Tris/HCl pH 7.8, 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 12 mM BMP, 2 M L-proline
Crystal Properties
Matthews coefficientSolvent content
2.4950.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.39α = 90
b = 116.84β = 90
c = 62.04γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-05-30MSINGLE 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
11.0519.799.90.0620.067114.96.64313041313.253
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)
11.051.199.71.0951.20.7141.915.978

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 REPLACEMENTTHROUGHOUT2QCD1.0519.7124005640899.820.12150.12060.1391RANDOM12.944
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]
0.85-0.4-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.961
r_dihedral_angle_4_deg18.345
r_dihedral_angle_3_deg13.322
r_rigid_bond_restr8.332
r_dihedral_angle_1_deg6.302
r_angle_other_deg2.305
r_angle_refined_deg1.783
r_chiral_restr0.111
r_bond_other_d0.035
r_gen_planes_other0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.961
r_dihedral_angle_4_deg18.345
r_dihedral_angle_3_deg13.322
r_rigid_bond_restr8.332
r_dihedral_angle_1_deg6.302
r_angle_other_deg2.305
r_angle_refined_deg1.783
r_chiral_restr0.111
r_bond_other_d0.035
r_gen_planes_other0.013
r_bond_refined_d0.011
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1962
Nucleic Acid Atoms
Solvent Atoms335
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction