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Crystal structure of PnrA from S. pneumoniae in complex with thymidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 28% PEG 600, 0.2 M calcium acetate and 0.1 M sodium cacodylate (pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.75 55.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.966 α = 90 b = 303.818 β = 90 c = 128.417 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 6M 2019-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979336 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.55 49.21 99.2 0.16 0.96 5.1 7.2 50223
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.63 0.71 0.52 1.5
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 2FQW 2.55 49.21 47620 2579 98.72 0.2108 0.2085 0.2117 0.2551 0.2545 RANDOM 47.42
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] 2.24 -0.28 -1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.266 r_dihedral_angle_3_deg 19.242 r_dihedral_angle_4_deg 15.337 r_dihedral_angle_1_deg 6.839 r_angle_refined_deg 1.495 r_angle_other_deg 1.263 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.266 r_dihedral_angle_3_deg 19.242 r_dihedral_angle_4_deg 15.337 r_dihedral_angle_1_deg 6.839 r_angle_refined_deg 1.495 r_angle_other_deg 1.263 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9852 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing