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Crystal structure of protein SP_0782 (7-79) from Streptococcus pneumoniae complexed with ssDNA. Northeast Structural Genomics Consortium (NESG) target SPR104
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 4.2 291 Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution:0.1M (NH4)2HPO4
0.1M Na3Citrate, PEG1K 40%, 3% Ethylene Glycol, macrobatch under oil, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.93 36.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.722 α = 90 b = 62.722 β = 90 c = 73.441 γ = 90
Symmetry Space Group P 41 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 MAR CCD 165 mm mirrors 2012-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.97915 NSLS X4C
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 2.9 48 92.2 0.097 7.7 1.9 11389 -3 40.32
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 3OBH 2.905 28.841 0.81 11389 6078 268 98.51 0.208 0.205 0.2067 0.263 0.2614 random 30.132
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] 1.543 1.543 -3.086
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.413 f_angle_d 1.327 f_chiral_restr 0.077 f_bond_d 0.009 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1099 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SCALEPACK data scaling BALBES phasing