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Crystal structure of Streptococcus pneumoniae SP_0782 (residues 7-79) in complex with single-stranded DNA dT12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OBH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 3.4 289 PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.63 24.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.319 α = 90 b = 66.319 β = 90 c = 39.083 γ = 90
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 PILATUS3 6M 2016-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.95 50 97 0.047 0.051 0.021 14.2 5.9 6092 17.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 84.3 0.281 0.312 0.132 0.962 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3OBH 1.951 23.626 1.55 5518 524 87.8 0.1843 0.1815 0.1826 0.21 0.2103 20.4138
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.096 f_angle_d 0.785 f_chiral_restr 0.051 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 529 Nucleic Acid Atoms 79 Solvent Atoms 49 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing