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Crystal structure of red abalone egg VERL repeat 2 with linker in complex with sperm lysin at 1.8 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5II8 PDB ID 5II8, 5II9, D_1200000737 experimental model PDB 5II9 PDB ID 5II8, 5II9, D_1200000737
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 5% (w/v) PEG 8000, 20% (v/v) PEG 300, 10% (v/v) Glycerol, 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.62 53.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.87 α = 90 b = 87.86 β = 100.93 c = 92.55 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 PILATUS 6M-F 2016-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.07227 ESRF ID29
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 45.322 99.5 0.05377 0.998 11.53 3.4 109995
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 1.864 99.6 1.494 0.307 0.97 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 PDB ID 5II8, 5II9, D_1200000737 1.8 45.322 1.33 109973 5503 99.55 0.2021 0.2008 0.205 0.227 0.2315
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 13.793 f_angle_d 0.793 f_chiral_restr 0.05 f_plane_restr 0.007 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7878 Nucleic Acid Atoms Solvent Atoms 559 Heterogen Atoms 94
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing Coot model building