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Crystal structure of nontypeable Haemophilus influenzae SapA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.4 295 0.1 M Tris pH 9.4, 1.5 M ammonium phosphate, 0.18 M sodium thiocyanate
Crystal Properties Matthews coefficient Solvent content 3.6 65.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.755 α = 90 b = 119.755 β = 90 c = 129.585 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 RAYONIX MX-300 2016-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.978560 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.25 44.014 99.9 0.089 0.091 0.021 0.998 16.1 19.2 45307
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 2.25 2.32 100 0.718 0.737 0.165 0.939 19.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.25 44.014 45239 2322 99.868 0.198 0.197 0.2048 0.225 0.2329 54.689
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] -0.113 -0.113 0.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.684 r_dihedral_angle_3_deg 15.632 r_dihedral_angle_2_deg 15.333 r_lrange_it 10.779 r_lrange_other 10.778 r_scangle_it 8.657 r_scangle_other 8.656 r_dihedral_angle_1_deg 7.093 r_mcangle_it 7.057 r_mcangle_other 7.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.684 r_dihedral_angle_3_deg 15.632 r_dihedral_angle_2_deg 15.333 r_lrange_it 10.779 r_lrange_other 10.778 r_scangle_it 8.657 r_scangle_other 8.656 r_dihedral_angle_1_deg 7.093 r_mcangle_it 7.057 r_mcangle_other 7.056 r_scbond_it 6.101 r_scbond_other 6.1 r_mcbond_other 5.399 r_mcbond_it 5.398 r_angle_refined_deg 1.691 r_angle_other_deg 0.622 r_nbd_refined 0.216 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.173 r_symmetry_nbd_refined 0.166 r_nbd_other 0.145 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_refined 0.075 r_symmetry_xyhbond_nbd_other 0.022 r_bond_other_d 0.012 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4152 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling BALBES phasing ARP/wARP model building PDB_EXTRACT data extraction