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X-ray crystal structure of NTHi Protein D bound to a putative glycerol moiety
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YDY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293.15 20% w/v PEG3000, 0.1 M Sodium Citrate pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.73 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.09 α = 90 b = 73.09 β = 90 c = 162.859 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS EIGER X 16M 2021-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979270 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 28 99.7 0.08 0.999 17.5 14.5 41845 37.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 96 2.6 0.394 0.98 13.6
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 1YDY 1.8 28 1.33 41750 2000 99.68 0.1561 0.1545 0.1549 0.1875 0.1879 44.24
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 13.4784 f_angle_d 1.0593 f_chiral_restr 0.0614 f_bond_d 0.0113 f_plane_restr 0.0091
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2696 Nucleic Acid Atoms Solvent Atoms 457 Heterogen Atoms 7
Software Software Software Name Purpose PHENIX refinement XDS data reduction pointless data scaling Aimless data scaling PHENIX phasing PHENIX model building Coot model building