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Structure of fertilization-blocking monoclonal antibody IE-3 VHVL bound to the ZP-N1 domain of mouse ZP2 (crystal form I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5II6 chain A residues P43-Q138 experimental model PDB 4AMK chain A (author H) residues Q3-S118 experimental model PDB 3MBX chain A (author L) residues D1-R114
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 24% (v/v) PEG 3350, 0.2 M sodium tartrate, 0.1 M Na-HEPES pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.99 38.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.64 α = 90 b = 92.29 β = 90 c = 91.17 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 PILATUS 6M-F 2014-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976251 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.53 29.164 98.5 0.03 0.016 1 18.6 3.3 115130 37.27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.58 99.2 1.376 0.721 0.55 1 3.4
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 P43-Q138 of PDB ID 5II6; chain H of PDB ID 4AMK; chain L of PDB ID 3MBX 1.53 29.16 1.5 109165 6384 93.38 0.2095 0.2058 0.2103 0.2329 0.237 36.88
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 11.6435 f_angle_d 0.5764 f_chiral_restr 0.0446 f_plane_restr 0.0035 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5152 Nucleic Acid Atoms Solvent Atoms 616 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection XDS data reduction XSCALE data scaling PHASER phasing PHENIX model building Coot model building