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Crystal structure of a dihydroorotase from Burkholderia cenocepacia J2315
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J79
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 289 0.1M Tris HCl, 18% PEG4000, 0.2M CaCl2, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.26 45.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.48 α = 90 b = 89.87 β = 90 c = 153.39 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 MARMOSAIC 225 mm CCD 2013-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.8 50 99.9 0.08 15.33 6.16 69475 69409 13.9
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 1.8 1.85 99.8 0.437 3.85 6.17 5049
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 1j79 1.8 46 65822 3510 99.91 0.15895 0.15745 0.1691 0.18714 0.1973 RANDOM 19.448
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] 0.63 0.14 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.734 r_dihedral_angle_4_deg 17.663 r_dihedral_angle_3_deg 10.75 r_dihedral_angle_1_deg 6.856 r_long_range_B_refined 4.76 r_long_range_B_other 4.61 r_scangle_other 2.539 r_mcangle_it 1.975 r_mcangle_other 1.975 r_angle_refined_deg 1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.734 r_dihedral_angle_4_deg 17.663 r_dihedral_angle_3_deg 10.75 r_dihedral_angle_1_deg 6.856 r_long_range_B_refined 4.76 r_long_range_B_other 4.61 r_scangle_other 2.539 r_mcangle_it 1.975 r_mcangle_other 1.975 r_angle_refined_deg 1.64 r_scbond_it 1.625 r_scbond_other 1.624 r_mcbond_it 1.273 r_mcbond_other 1.272 r_angle_other_deg 0.864 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 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 5354 Nucleic Acid Atoms Solvent Atoms 598 Heterogen Atoms 16
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling