☰ Navigation Tabs
Covalent complex of orotidine 5'-monophosphate decarboxylase (ODCase) with 6-Iodo-UMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KM1 1KM1(location), 1DV7(model) experimental model PDB 1DV7 1KM1(location), 1DV7(model)
Crystallization Crystal Properties Matthews coefficient Solvent content 2.03 39.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.163 α = 90 b = 74.063 β = 119.39 c = 59.243 γ = 90
Symmetry Space Group P 1 21 1
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 4 2004-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D 0.9795 APS 14-BM-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.6 100 99.9 0.051 26.1 3.8 57752 1 15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 99.9 0.303
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 1KM1(location), 1DV7(model) 1.6 23.97 57709 2839 99.8 0.162 0.162 0.1736 0.187 0.1952 The same set with 1x1z 16.6
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] 1.48 -0.61 0.81 -2.3
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 3.48 c_scbond_it 2.32 c_mcangle_it 1.61 c_angle_deg 1.6 c_improper_angle_d 1.28 c_mcbond_it 0.98 c_bond_d 0.014 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 3.48 c_scbond_it 2.32 c_mcangle_it 1.61 c_angle_deg 1.6 c_improper_angle_d 1.28 c_mcbond_it 0.98 c_bond_d 0.014 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3260 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 66
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing