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Crystal structure of Human Orotidine 5'-monophosphate Decarboxylase complexed with BMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P1F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.4 293 Ammonium Sulfate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.596 α = 90 b = 116.886 β = 90 c = 61.985 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 ADSC QUANTUM 315 2007-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.90020 APS 14-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.93 50 95.3 0.13 0.13 7.5 7 21306 20304
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) 1.93 1.96 74.6 0.5 0.5 2.18 5.6 818
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2P1F 1.93 50 21306 19516 1048 95.15 0.18274 0.18126 0.1823 0.21068 0.208 RANDOM 27.081
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] 5.44 -2.37 -3.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.096 r_dihedral_angle_4_deg 17.653 r_dihedral_angle_3_deg 12.678 r_dihedral_angle_1_deg 6.345 r_scangle_it 4.14 r_scbond_it 2.587 r_angle_refined_deg 1.546 r_mcangle_it 1.451 r_mcbond_it 1.034 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.096 r_dihedral_angle_4_deg 17.653 r_dihedral_angle_3_deg 12.678 r_dihedral_angle_1_deg 6.345 r_scangle_it 4.14 r_scbond_it 2.587 r_angle_refined_deg 1.546 r_mcangle_it 1.451 r_mcbond_it 1.034 r_nbtor_refined 0.306 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.108 r_symmetry_hbond_refined 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2025 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing Coot model building