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CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF FIBRONECTIN- BINDING PROTEIN PAVA FROM STREPTOCOCCUS PNEUMONIAE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 27% (w/v) PEG 4000, 0.2 M Ammonium
Acetate, 0.1 M Sodium Citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.49 50.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.873 α = 90 b = 46.814 β = 90.931 c = 83.678 γ = 90
Symmetry Space Group P 1 21 1
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 200K 2018-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.395 83.667 99 0.11 0.06 7.1 3.26 23361 25.5368070055
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 2.395 2.44 0.272 0.841
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 FREE R-VALUE 5H3X 2.395 41.83 1.34 23359 1141 99.2732681683 0.17 0.1665 0.1682 0.237 0.2382 26.5245750125
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 15.6166387629 f_angle_d 0.904834061269 f_chiral_restr 0.0522595940258 f_bond_d 0.0080965372865 f_plane_restr 0.00499847624697
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4188 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing