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Crystal Structure of PitA fragment from pilus islet-2 of Streptococcus oralis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VCN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 295 0.2 M ammonium acetate 0.1 M HEPES pH 7.2, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.22 61.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.48 α = 80.087 b = 70.875 β = 87.024 c = 82.466 γ = 87.7
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 2018-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97951 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 81.15 90.3 0.052 0.047 0.999 11.3 3.2 83573
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.04 92.1 0.818 0.647 0.727 1.3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7VCN 2 69.879 83565 4294 90.314 0.203 0.2009 0.2339 0.2264 57.196
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] 3.402 -1.455 0.52 -0.696 0.411 -2.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.5 r_dihedral_angle_4_deg 19.342 r_dihedral_angle_3_deg 15.642 r_lrange_it 11.076 r_scangle_it 8.553 r_dihedral_angle_1_deg 7.078 r_scbond_it 5.847 r_mcangle_it 5.766 r_mcbond_it 4.09 r_angle_refined_deg 1.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.5 r_dihedral_angle_4_deg 19.342 r_dihedral_angle_3_deg 15.642 r_lrange_it 11.076 r_scangle_it 8.553 r_dihedral_angle_1_deg 7.078 r_scbond_it 5.847 r_mcangle_it 5.766 r_mcbond_it 4.09 r_angle_refined_deg 1.925 r_nbtor_refined 0.306 r_nbd_refined 0.196 r_symmetry_nbd_refined 0.19 r_symmetry_xyhbond_nbd_refined 0.144 r_chiral_restr 0.139 r_xyhbond_nbd_refined 0.129 r_ncsr_local_group_1 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7586 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing