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Covalent complex of orotidine monophosphate decarboxylase D70A mutant from M. thermoautotrophicus with 6-cyano-UMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X1Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 1.2-1.36M Sodium Citrate, 5% dioxiane, pH 6.0-8.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.02 39.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.076 α = 90 b = 73.769 β = 119.4 c = 59.152 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 CCD MAR CCD 165 mm default 2004-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.127 APS 14-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 100 87.9 0.063 18.3 3.62 38640 13.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 57 0.273 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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1x1z 1.8 22.19 38632 1907 96.1 0.162 0.1778 0.191 0.1758 same flag 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] 0.74 -0.79 2.26 -2.99
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.3 c_scangle_it 4.62 c_scbond_it 3.19 c_mcangle_it 1.91 c_angle_deg 1.5 c_mcbond_it 1.28 c_improper_angle_d 1.18 c_bond_d 0.013 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.3 c_scangle_it 4.62 c_scbond_it 3.19 c_mcangle_it 1.91 c_angle_deg 1.5 c_mcbond_it 1.28 c_improper_angle_d 1.18 c_bond_d 0.013 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 3254 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 66
Software Software Software Name Purpose CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing