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Crystal Structure of PitA from pilus islet-2 of Streptococcus oralis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VCR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 295 100 mM HEPES pH 7.8, 1 M potassium iodide, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.04 59.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.271 α = 90 b = 422.928 β = 90 c = 48.391 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 225 mm CCD 2016-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.7712 ESRF BM14
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 2.984 51.93 95 0.072 0.991 10.6 7 20771
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 2.984 3.068 0.479 0.577 1.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7VCR 2.984 51.93 20771 1068 90.125 0.256 0.2533 0.254 0.3052 0.3052 85.705
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] 2.478 -0.729 -1.749
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.567 r_dihedral_angle_4_deg 20.79 r_dihedral_angle_3_deg 19.753 r_lrange_it 15.007 r_mcangle_it 6.931 r_scangle_it 6.744 r_dihedral_angle_1_deg 6.553 r_mcbond_it 4.041 r_scbond_it 3.981 r_angle_refined_deg 1.558
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.567 r_dihedral_angle_4_deg 20.79 r_dihedral_angle_3_deg 19.753 r_lrange_it 15.007 r_mcangle_it 6.931 r_scangle_it 6.744 r_dihedral_angle_1_deg 6.553 r_mcbond_it 4.041 r_scbond_it 3.981 r_angle_refined_deg 1.558 r_symmetry_nbd_refined 0.373 r_nbtor_refined 0.31 r_metal_ion_refined 0.297 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.105 r_symmetry_xyhbond_nbd_refined 0.095 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5878 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing