4HIB

Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with CMP-N4-OH


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52931.6M-1.7M Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0941.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.78α = 90
b = 61.64β = 112.08
c = 71.37γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDDCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing2011-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.979490CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.5450850.04613.9670712-331.727
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.541.5832.70.0150.44

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 REPLACEMENTTHROUGHOUT2qcm1.866.0850390263399.020.19520.190.223RANDOM29.1315
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]
1.441.81-1.681.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.426
r_dihedral_angle_4_deg19.76
r_dihedral_angle_3_deg14.676
r_dihedral_angle_1_deg6.443
r_scangle_it5.262
r_scbond_it3.667
r_angle_refined_deg2.215
r_mcangle_it2.177
r_mcbond_it1.364
r_chiral_restr0.268
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.426
r_dihedral_angle_4_deg19.76
r_dihedral_angle_3_deg14.676
r_dihedral_angle_1_deg6.443
r_scangle_it5.262
r_scbond_it3.667
r_angle_refined_deg2.215
r_mcangle_it2.177
r_mcbond_it1.364
r_chiral_restr0.268
r_bond_refined_d0.028
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3916
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms52

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Macromoleculardata collection