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2.4 Angstrom Crystal Structure of Dihydroorotase (pyrC) from Campylobacter jejuni.
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 6.5 295 Protein: 7.7 mg/mL, 0.25M Sodium cloride, Tris-HCl (pH 8.3);
Screen: PACT (F9), 0.2M Potassium/Sodium tartrate, 0.1M Bis TRIS propane (pH 6.5), 20% w/v PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.64 53.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.52 α = 90 b = 80.802 β = 90 c = 154.878 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 300 mm CCD Beryllium lenses 2010-11-12 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 2.4 30 100 0.079 25 7.4 35063 35063 -3 51.2
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) 2.4 2.44 100 0.559 3.8 7.5 1709
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1J79 2.4 29.52 33099 33099 1754 99.98 0.19351 0.19351 0.19065 0.24954 0.2533 RANDOM 42.677
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] 0.99 3.09 -4.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.512 r_dihedral_angle_3_deg 9.801 r_dihedral_angle_4_deg 9.288 r_scangle_it 4.97 r_scbond_it 3.186 r_dihedral_angle_1_deg 2.823 r_mcangle_it 2.225 r_angle_refined_deg 1.46 r_mcbond_it 1.201 r_angle_other_deg 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.512 r_dihedral_angle_3_deg 9.801 r_dihedral_angle_4_deg 9.288 r_scangle_it 4.97 r_scbond_it 3.186 r_dihedral_angle_1_deg 2.823 r_mcangle_it 2.225 r_angle_refined_deg 1.46 r_mcbond_it 1.201 r_angle_other_deg 0.86 r_mcbond_other 0.263 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5439 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 14
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling