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Orotidine Monophosphate Decarboxylase K72A mutant from M. thermoautotrophicum complexed 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 1.2-1.36M Sodium Citrate, 5% dioxiane, pH 6.0-8.5, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.03 39.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.086 α = 90 b = 73.819 β = 119.3 c = 59.323 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 2004-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.0332 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 1.53 100 95.6 0.055 22.1 62518 14
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 1.53 1.56 0.299 2.8
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 FOURIER SYNTHESIS THROUGHOUT 1x1z 1.53 51.99 59403 3091 95.49 0.16085 0.15947 0.1591 0.1873 0.1627 same flag with 1x1z 14.179
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] 0.04 -0.23 0.26 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.899 r_dihedral_angle_4_deg 20.019 r_dihedral_angle_3_deg 11.696 r_dihedral_angle_1_deg 5.465 r_scangle_it 4.736 r_scbond_it 2.931 r_angle_refined_deg 1.646 r_mcangle_it 1.62 r_mcbond_it 1.133 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.899 r_dihedral_angle_4_deg 20.019 r_dihedral_angle_3_deg 11.696 r_dihedral_angle_1_deg 5.465 r_scangle_it 4.736 r_scbond_it 2.931 r_angle_refined_deg 1.646 r_mcangle_it 1.62 r_mcbond_it 1.133 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.218 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.125 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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 3252 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing