3MW7

Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with 5-fluoro-UMP(produced from 5-fluoro-6-amino-UMP)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2P1F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.4293Ammonium Sulfate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1141.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.29α = 90
b = 61.742β = 111.64
c = 71.212γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 1-BM-C0.90020APS1-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.35083.50.1060.10610.23.32067519597
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3449.80.330.331.841.8626

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 REPLACEMENTTHROUGHOUT2P1F2.325019597106582.970.207580.204520.26532RANDOM35.443
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]
4.016.55-3.194
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.446
r_dihedral_angle_4_deg18.136
r_dihedral_angle_3_deg17.808
r_dihedral_angle_1_deg6.817
r_scangle_it3.533
r_scbond_it2.191
r_angle_refined_deg1.606
r_mcangle_it1.46
r_mcbond_it0.898
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.446
r_dihedral_angle_4_deg18.136
r_dihedral_angle_3_deg17.808
r_dihedral_angle_1_deg6.817
r_scangle_it3.533
r_scbond_it2.191
r_angle_refined_deg1.606
r_mcangle_it1.46
r_mcbond_it0.898
r_nbtor_refined0.306
r_symmetry_hbond_refined0.23
r_symmetry_vdw_refined0.221
r_nbd_refined0.219
r_xyhbond_nbd_refined0.16
r_chiral_restr0.105
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3937
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms44

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling