3G3M

Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 5-fluoro-6-iodo-UMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2P1FPDB ENTRY 2P1F

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.4293Ammonium Sulfate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3247.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.28α = 90
b = 116.558β = 90
c = 62.113γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDDCM WITH CRYO-COOLED 1ST CRYSTAL SAGITTALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR2007-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-1CLSI08ID-1

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
11.45093.10.0570.05715.46.150630
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)
1.41.4560.70.2130.2133.53.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2P1F1.450496202643930.160070.158910.1815RANDOM15.312
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]
1.65-0.94-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.879
r_dihedral_angle_4_deg13.428
r_dihedral_angle_3_deg12.444
r_dihedral_angle_1_deg6.435
r_scangle_it4.823
r_scbond_it3.196
r_angle_refined_deg2.423
r_mcangle_it1.872
r_mcbond_it1.191
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.879
r_dihedral_angle_4_deg13.428
r_dihedral_angle_3_deg12.444
r_dihedral_angle_1_deg6.435
r_scangle_it4.823
r_scbond_it3.196
r_angle_refined_deg2.423
r_mcangle_it1.872
r_mcbond_it1.191
r_nbtor_refined0.306
r_symmetry_vdw_refined0.233
r_nbd_refined0.222
r_chiral_restr0.165
r_symmetry_hbond_refined0.136
r_xyhbond_nbd_refined0.132
r_bond_refined_d0.025
r_gen_planes_refined0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2239
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms22

Software

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