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Re-refinement of 4dd4; cisplatin coordination chemistry determination at hen egg white lysozyme His15 with standard uncertainties
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DD4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 4.7 295 CRYSTALLIZATION CONDITIONS: HEWL CO-CRYSTALLIZED WITH CISPLATIN IN
462.5 microL 0.05 M SODIUM ACETATE AND 462.5 microL 10% SODIUM CHLORIDE
IN 75 microL DMSO MEDIA, PH 4.7, BATCH, TEMPERATURE 295K.
Crystal Properties Matthews coefficient Solvent content 2.01 38.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.832 α = 90 b = 78.832 β = 90 c = 37.021 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 CCD Bruker Platinum 135 INCOATEC HELIOS CONFOCAL OPTICS 2011-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 24.93 88.59 0.079 22.2 14.6 11826
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.761 100 0.313 5.2 9.1
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 FREE R-VALUE 4dd4 1.7 24.929 1.34 11824 582 88.58 0.2041 0.202 0.2059 0.2476 0.2529 12.6
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 12.871 f_angle_d 0.719 f_chiral_restr 0.026 f_bond_d 0.005 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 20
Software Software Software Name Purpose PHASER phasing PHENIX refinement