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Orotidine Monophosphate Deacarboxylase D70A/K72A double mutant from M. thermoautotrophicum complexed with 6- cyano-UMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E6Y
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 1.95 36.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.556 α = 90 b = 64.359 β = 115.52 c = 61.539 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 ADSC QUANTUM 315 default 2006-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
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 1.56 100 83.9 0.083 9.9 3.6 50081
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 1.56 1.59 30.2 0.43 1.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2E6Y 1.56 55.56 47506 2544 83.87 0.16118 0.15976 0.18679 0.1828 RANDOM 18.72
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] -1.21 -1.05 0.22 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.8 r_dihedral_angle_4_deg 17.485 r_dihedral_angle_3_deg 14.492 r_dihedral_angle_1_deg 6.033 r_scangle_it 5.372 r_scbond_it 3.321 r_mcangle_it 1.855 r_angle_refined_deg 1.793 r_mcbond_it 1.258 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.8 r_dihedral_angle_4_deg 17.485 r_dihedral_angle_3_deg 14.492 r_dihedral_angle_1_deg 6.033 r_scangle_it 5.372 r_scbond_it 3.321 r_mcangle_it 1.855 r_angle_refined_deg 1.793 r_mcbond_it 1.258 r_nbtor_refined 0.311 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.171 r_chiral_restr 0.128 r_xyhbond_nbd_refined 0.124 r_symmetry_hbond_refined 0.114 r_bond_refined_d 0.021 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 3220 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing