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Zr(IV)-substituted Keggin directly binding to the side chain of Hen Egg-White Lysozyme (HEWL)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LYZ pdbid 1LYZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 289 1.75 mM HEWL, 0.88 mM 2:2 Zr(IV)-Keggin, 1.5 M NH4Cl, 0.1 M Bis-Tris propane pH = 7.0
Crystal Properties Matthews coefficient Solvent content 1.99 38.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.701 α = 90 b = 77.701 β = 90 c = 37.866 γ = 90
Symmetry Space Group P 43 21 2
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 2017-05-18 M MAD 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000 SLS X06DA 2 SYNCHROTRON SLS BEAMLINE X06DA 1.210 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.23 38.85 100 0.039 0.042 0.015 1 32.4 7 34264 13.26
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 1.23 1.25 100 0.551 0.595 0.222 0.893 7.1
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 THROUGHOUT pdbid 1LYZ 1.23 38.85 1.34 64188 3260 99.78 0.1487 0.1475 0.188 0.1713 0.2079 19.0469
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 12.361 f_angle_d 1.266 f_chiral_restr 0.089 f_bond_d 0.015 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 159
Software Software Software Name Purpose HKL-2000 data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction