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Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 mM Rose Bengal and 10mM H2PtCl6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 193L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 0.7M NaCl, 0.1 M acetate buffer
Crystal Properties Matthews coefficient Solvent content 1.97 37.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.458 α = 90 b = 78.458 β = 90 c = 36.647 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 RIGAKU JUPITER 210 2017-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.88 55.48 99.48 18.7 13.1 9257
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.92 99.86 24.28 9.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 193L 1.88 55.48 9257 480 99.48 0.18454 0.18157 0.1931 0.23748 0.2482 RANDOM 33.867
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.225 r_dihedral_angle_4_deg 24.271 r_dihedral_angle_3_deg 15.217 r_long_range_B_other 7.891 r_long_range_B_refined 7.884 r_dihedral_angle_1_deg 6.94 r_scangle_other 6.564 r_scbond_it 4.338 r_scbond_other 4.332 r_mcangle_other 3.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.225 r_dihedral_angle_4_deg 24.271 r_dihedral_angle_3_deg 15.217 r_long_range_B_other 7.891 r_long_range_B_refined 7.884 r_dihedral_angle_1_deg 6.94 r_scangle_other 6.564 r_scbond_it 4.338 r_scbond_other 4.332 r_mcangle_other 3.684 r_mcangle_it 3.681 r_mcbond_it 2.885 r_mcbond_other 2.875 r_angle_refined_deg 1.815 r_angle_other_deg 1.166 r_chiral_restr 0.126 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing