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X-ray structure of meningococcal factor H binding protein variant 2 in complex with a specific and bactericidal human monoclonal antibody 1B1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XZW 6XZW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.09M Sodium Nitrate, Sodium Phosphate dibasic, Ammonium Solphate, 0.1 M Buffer Imidazole, MES monohydrate, pH6.5 and as precipitant mix 25% v/v MPD, 25% PEG 100, 25% w/v PEG 3350.
Crystal Properties Matthews coefficient Solvent content 3.17 61.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.153 α = 90 b = 135.641 β = 105.18 c = 121.53 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 150 PIXEL DECTRIS PILATUS3 2M 2017-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.966 ESRF BM30A
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 2.41 49.66 99.7 0.997 10 3.5 92813 62.03
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 2.41 2.49 0.494
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6XZW 2.41 49.66 1.34 92645 4732 99.58 0.2076 0.2044 0.2696 0.2687 65.98
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 16.5108 f_angle_d 0.9894 f_chiral_restr 0.0558 f_bond_d 0.0079 f_plane_restr 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13487 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 83
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing