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Snapshot of the reaction from 6-CN-UMP to BMP catalyzed by Orotidine Monophosphate Deacarboxylase from M. thermoautotrophicum
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 2.02 38.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.024 α = 90 b = 73.543 β = 119.29 c = 59.331 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 4 default 2003-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9000 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 1.57 100 99.7 0.06 22.1 3.8 60802 14.4
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 1.57 1.6 99.8 0.296 5
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 1.57 51.99 57489 2979 99.63 0.15685 0.15551 0.1559 0.18249 0.1596 same flag with 1x1z 15.243
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] 0.29 -0.33 0.26 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.448 r_dihedral_angle_4_deg 18.724 r_dihedral_angle_3_deg 12.004 r_dihedral_angle_1_deg 5.48 r_scangle_it 4.854 r_scbond_it 2.98 r_mcangle_it 1.728 r_angle_refined_deg 1.677 r_mcbond_it 1.133 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.448 r_dihedral_angle_4_deg 18.724 r_dihedral_angle_3_deg 12.004 r_dihedral_angle_1_deg 5.48 r_scangle_it 4.854 r_scbond_it 2.98 r_mcangle_it 1.728 r_angle_refined_deg 1.677 r_mcbond_it 1.133 r_nbtor_refined 0.317 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.122 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.114 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 3260 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing