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Crystal structure of Methanothermobacter thermautotrophicus orotidine 5'-monophosphate decarboxylase complexed with pyrazofurin monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DV7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 293 Trisodium Citrate, Dioxane, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.244 α = 90 b = 103.574 β = 90 c = 73.739 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 100 CCD ADSC QUANTUM 315 2006-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.90020 APS 14-BM-C
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 1.7 50 99.9 0.084 11.7 9.6 24704
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 1.7 1.73 99.7 0.489 4.43 7.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1DV7 1.7 50 24027 648 99.66 0.15661 0.15584 0.1556 0.18683 0.1872 RANDOM 17.911
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] 0.4 -0.75 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.238 r_dihedral_angle_4_deg 18.547 r_dihedral_angle_3_deg 15.164 r_dihedral_angle_1_deg 5.687 r_scangle_it 3.857 r_scbond_it 2.508 r_angle_refined_deg 1.564 r_mcangle_it 1.476 r_mcbond_it 0.963 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.238 r_dihedral_angle_4_deg 18.547 r_dihedral_angle_3_deg 15.164 r_dihedral_angle_1_deg 5.687 r_scangle_it 3.857 r_scbond_it 2.508 r_angle_refined_deg 1.564 r_mcangle_it 1.476 r_mcbond_it 0.963 r_nbtor_refined 0.313 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.147 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.103 r_symmetry_hbond_refined 0.1 r_bond_refined_d 0.011 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1622 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 28
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling