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Factor H enhancing human antibody fragment (Fab) to meningococcal Factor H binding protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KVD homology model constructed from human Fab; FHbp ID 1 (3KVD)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 HEPES, polyethylene glycol 3350, tryptone, sodium azide
Crystal Properties Matthews coefficient Solvent content 2.31 46.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.58 α = 90 b = 86.03 β = 96.907 c = 107.89 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 S 6M 2020-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11583 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2 107.11 94.96 0.101 0.123 0.071 8.02 2.7 46166 45.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 82.44 1.66 2.09 1.24 2.4
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 homology model constructed from human Fab; FHbp ID 1 (3KVD) 2 107.11 1.34 44971 1571 94.96 0.2356 0.234 0.242 0.2814 0.2826 61.91
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 19.7465 f_angle_d 1.1211 f_chiral_restr 0.072 f_bond_d 0.008 f_plane_restr 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5057 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms
Software Software Software Name Purpose Coot refinement PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing