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1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein PruR (Atu3496) from Agrobacterium fabrum str. C58
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KOM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 Protein: 12.5 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3.
Screen: JCSG+ (F8), 2.1M DL-Malic acid pH 7.0;
Cryo: 25% PEG 400, 1.5M DL-Malic acid pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.85 56.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.928 α = 90 b = 62.022 β = 90 c = 101.916 γ = 90
Symmetry Space Group P 21 21 2
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 Be 2019-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.83 30 100 0.084 0.084 0.093 0.04 0.999 19.4 5.4 68046 -3 20.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.86 100 0.773 0.773 0.857 0.367 0.78 2.2 5.4
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 7kom 1.83 29.8 64577 3422 99.68 0.1635 0.1619 0.1728 0.1933 0.2011 RANDOM 23.732
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] -1.27 -1.09 2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.694 r_dihedral_angle_4_deg 15.261 r_dihedral_angle_3_deg 9.97 r_dihedral_angle_1_deg 4.426 r_angle_refined_deg 1.364 r_angle_other_deg 0.358 r_chiral_restr 0.062 r_gen_planes_refined 0.056 r_gen_planes_other 0.053 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.694 r_dihedral_angle_4_deg 15.261 r_dihedral_angle_3_deg 9.97 r_dihedral_angle_1_deg 4.426 r_angle_refined_deg 1.364 r_angle_other_deg 0.358 r_chiral_restr 0.062 r_gen_planes_refined 0.056 r_gen_planes_other 0.053 r_bond_refined_d 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4546 Nucleic Acid Atoms Solvent Atoms 735 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing