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Crystal structure of human orotidine 5'-monophosphate decarboxylase covalently modified by 2'-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 VAPOR DIFFUSION, HANGING DROP 7.5 293 Sodium Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 46.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.499 α = 90 b = 116.035 β = 90 c = 62.103 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. 2007-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97934 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 1.35 50 94.1 0.073 0.073 11.2 4.8 58884 56107
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) 1.35 1.4 97.7 0.476 0.476 3.1 4.4 6052
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 1.35 23.61 55868 2994 94.04 0.15636 0.15533 0.1536 0.17534 0.1721 RANDOM 13.982
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] 1.01 -0.65 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.419 r_dihedral_angle_4_deg 13.277 r_dihedral_angle_3_deg 12.575 r_dihedral_angle_1_deg 6.129 r_scangle_it 3.558 r_scbond_it 2.21 r_angle_refined_deg 1.439 r_mcangle_it 1.327 r_mcbond_it 0.95 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.419 r_dihedral_angle_4_deg 13.277 r_dihedral_angle_3_deg 12.575 r_dihedral_angle_1_deg 6.129 r_scangle_it 3.558 r_scbond_it 2.21 r_angle_refined_deg 1.439 r_mcangle_it 1.327 r_mcbond_it 0.95 r_nbtor_refined 0.305 r_nbd_refined 0.251 r_symmetry_hbond_refined 0.222 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1974 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 27
Software Software Software Name Purpose MxDC data collection MOLREP phasing REFMAC refinement Coot model building HKL-2000 data reduction HKL-2000 data scaling