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Crystal structure of orotate phosphoribosyltransferase (OPRTase) from Burkholderia cenocepacia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M3H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 JCSG+ g6: 200mM sodium malonate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.54 51.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.31 α = 105.83 b = 82.97 β = 104.27 c = 83.1 γ = 117.36
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 RAYONIX MX225HE 2013-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97872 APS 21-ID-G
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 1.85 97.4 0.06 17.9 3.9 134209 130679 17.7
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 1.85 1.9 95.8 0.502 2.75 3.6 9459
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 3m3h 1.85 50 124114 6564 97.62 0.15758 0.15556 0.1665 0.19659 0.2049 RANDOM 25.629
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] 0.06 0.24 0.51 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.289 r_dihedral_angle_4_deg 18.029 r_dihedral_angle_3_deg 12.985 r_long_range_B_refined 7.787 r_long_range_B_other 7.786 r_dihedral_angle_1_deg 6.039 r_mcangle_it 1.665 r_mcangle_other 1.665 r_angle_refined_deg 1.573 r_scangle_other 1.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.289 r_dihedral_angle_4_deg 18.029 r_dihedral_angle_3_deg 12.985 r_long_range_B_refined 7.787 r_long_range_B_other 7.786 r_dihedral_angle_1_deg 6.039 r_mcangle_it 1.665 r_mcangle_other 1.665 r_angle_refined_deg 1.573 r_scangle_other 1.462 r_mcbond_it 1.004 r_mcbond_other 0.991 r_scbond_it 0.921 r_scbond_other 0.921 r_angle_other_deg 0.852 r_chiral_restr 0.099 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10303 Nucleic Acid Atoms Solvent Atoms 1175 Heterogen Atoms 56
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling