6ZX1

OMPD-domain of human UMPS in complex with 6-Aza-UMP at 1.0 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 8.0, 1.6 - 1.8 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol Cryo-protection: 100 mM Tris/HCl pH 8.0, 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 1 M L-proline, 25 mM 6-Aza-UMP
Crystal Properties
Matthews coefficientSolvent content
2.4850.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.67α = 90
b = 116.57β = 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 16M2018-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.72930PETRA 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
1119.6897.70.0450.052114.653.85114753811.851
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)
111.0598.80.7860.9090.6151.783.813

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 REPLACEMENTTHROUGHOUT2QCD119.68140278726097.650.12280.1220.1376RANDOM11.243
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]
0.24-0.15-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.243
r_dihedral_angle_4_deg19.12
r_dihedral_angle_3_deg12.627
r_rigid_bond_restr8.744
r_dihedral_angle_1_deg6.515
r_angle_other_deg2.284
r_angle_refined_deg1.675
r_chiral_restr0.095
r_bond_other_d0.034
r_gen_planes_other0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.243
r_dihedral_angle_4_deg19.12
r_dihedral_angle_3_deg12.627
r_rigid_bond_restr8.744
r_dihedral_angle_1_deg6.515
r_angle_other_deg2.284
r_angle_refined_deg1.675
r_chiral_restr0.095
r_bond_other_d0.034
r_gen_planes_other0.011
r_bond_refined_d0.01
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1959
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms42

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction