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Crystal structure of potent neutralizing antibody m336 in complex with MERS Co-V RBD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KQZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20% PEG 2000MME, 100 mM HEPES, pH7.5
Crystal Properties Matthews coefficient Solvent content 2.27 45.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.795 α = 90 b = 146.879 β = 90 c = 200.508 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 CCD MARMOSAIC 300 mm CCD MAR300HS 2014-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 2.45 50 91.5 0.114 0.129 0.06 6.3 3.7 48854 -3 47.67
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 2.45 2.49 52.6 0.475 0.555 0.278 0.798 1.3 2.5 1381
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4KQZ 2.45 45.449 1.36 48806 2479 91.51 0.2008 0.1982 0.2069 0.2491 0.2566 Random selection 67.0747
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 10.376 f_angle_d 0.624 f_chiral_restr 0.024 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9745 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 68
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction Coot model building SCALEPACK data scaling