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Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 5-fluoro-6-iodo-UMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P1F PDB ENTRY 2P1F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.4 293 Ammonium Sulfate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 47.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.28 α = 90 b = 116.558 β = 90 c = 62.113 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD DCM WITH CRYO-COOLED 1ST CRYSTAL SAGITTALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR 2007-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 CLSI 08ID-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.4 50 93.1 0.057 0.057 15.4 6.1 50630
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) Redundancy Number Unique Reflections (All) 1.4 1.45 60.7 0.213 0.213 3.5 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2P1F 1.4 50 49620 2643 93 0.16007 0.15891 0.1613 0.1815 0.1819 RANDOM 15.312
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.879 r_dihedral_angle_4_deg 13.428 r_dihedral_angle_3_deg 12.444 r_dihedral_angle_1_deg 6.435 r_scangle_it 4.823 r_scbond_it 3.196 r_angle_refined_deg 2.423 r_mcangle_it 1.872 r_mcbond_it 1.191 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.879 r_dihedral_angle_4_deg 13.428 r_dihedral_angle_3_deg 12.444 r_dihedral_angle_1_deg 6.435 r_scangle_it 4.823 r_scbond_it 3.196 r_angle_refined_deg 2.423 r_mcangle_it 1.872 r_mcbond_it 1.191 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.233 r_nbd_refined 0.222 r_chiral_restr 0.165 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.132 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 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 Atoms Number Protein Atoms 2239 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 22
Software Software Software Name Purpose MxDC data collection MOLREP phasing REFMAC refinement Coot model building HKL-2000 data reduction HKL-2000 data scaling