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Crystal structure of orotidine 5-phosphate decarboxylase from Anaerococcus prevotii DSM 20548
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 297 0.2M NaCl, 0.1 M Tris pH 7.0, 30% (w/v) PEG-3000, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.23 44.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.507 α = 90 b = 108.848 β = 90 c = 138.171 γ = 90
Symmetry Space Group P 21 21 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 315r 2010-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97924 APS 19-ID
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 1.844 85.503 94.2 0.114 30.7 7.7 52163 49114 -3
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) 1.844 1.88 92.9 0.774 2.72 6.2 2412
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 1.844 85.5 48644 48644 2488 93.37 0.1604 0.1604 0.1584 0.1655 0.197 0.2029 RANDOM 19.769
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] 0.33 0.47 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.039 r_dihedral_angle_4_deg 23.82 r_dihedral_angle_3_deg 13.706 r_dihedral_angle_1_deg 5.676 r_scangle_it 4.209 r_scbond_it 2.568 r_angle_refined_deg 1.388 r_mcangle_it 1.377 r_mcbond_it 0.761 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.039 r_dihedral_angle_4_deg 23.82 r_dihedral_angle_3_deg 13.706 r_dihedral_angle_1_deg 5.676 r_scangle_it 4.209 r_scbond_it 2.568 r_angle_refined_deg 1.388 r_mcangle_it 1.377 r_mcbond_it 0.761 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4604 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MLPHARE phasing DM phasing SHELXDE phasing RESOLVE phasing ARP/wARP model building Coot model building