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Haemophilus parainfluenzae Holo HphA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OM5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Microseeding using seed stock obtained from 2.4 M sodium malonate pH 7.0 into final hit condition: 0.1M Tris-HCl pH 8.52 and 2M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.85 56.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.402 α = 90 b = 50.313 β = 90 c = 125.899 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2021-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979328 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.937 39.3 99.81 0.998 12.23 11.3 24073
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.937 2.006 0.892
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.937 39.3 1.35 24037 1277 99.82 0.1856 0.183 0.1867 0.2329 0.2357
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 13.562 f_angle_d 1.563 f_chiral_restr 0.072 f_bond_d 0.016 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1925 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 44
Software Software Software Name Purpose autoPROC data processing pointless data scaling Aimless data scaling STARANISO data scaling PHENIX phasing PHENIX refinement autoPROC data reduction XDS data reduction