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Orotidine Monophosphate Decarboxylase K72A mutant complexed with BMP (produced from 6-Iodo-UMP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X1Z ODCase from M. thermoautotrophicum
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 2.01 38.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.933 α = 90 b = 103.29 β = 90 c = 73.533 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 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 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 1.58 200 99.9 0.057 33.2 7.3 30641
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 1.58 1.61 100 0.301 7
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 ODCase from M. thermoautotrophicum 1.58 51.64 28996 1518 99.67 0.15251 0.15155 0.1509 0.1708 0.1726 RANDOM 13.881
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] 0.35 -0.73 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.423 r_dihedral_angle_4_deg 19.829 r_dihedral_angle_3_deg 13.173 r_dihedral_angle_1_deg 5.498 r_scangle_it 4.476 r_scbond_it 2.781 r_angle_refined_deg 1.609 r_mcangle_it 1.538 r_mcbond_it 1.035 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.423 r_dihedral_angle_4_deg 19.829 r_dihedral_angle_3_deg 13.173 r_dihedral_angle_1_deg 5.498 r_scangle_it 4.476 r_scbond_it 2.781 r_angle_refined_deg 1.609 r_mcangle_it 1.538 r_mcbond_it 1.035 r_nbtor_refined 0.313 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.157 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.112 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 1626 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing