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Crystal structure of hen egg white lysozyme soaked with 100mM RhCl3 at pH2.2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 193L PDB ENTRY 193L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.97 37.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.967 α = 90 b = 77.967 β = 90 c = 37.14 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 IMAGE PLATE RIGAKU RAXIS VII 2008-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.75 80 96.1 0.065 21.5 11665 22.778
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) 1.75 1.81 98 0.325 21.5
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 PDB ENTRY 193L 1.75 18.38 11069 563 96.26 0.19526 0.19376 0.1913 0.2245 0.2262 RANDOM 19.6
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 r_dihedral_angle_2_deg 33.592 r_dihedral_angle_4_deg 14.32 r_dihedral_angle_3_deg 13.6 r_sphericity_free 8.579 r_dihedral_angle_1_deg 5.883 r_scangle_it 3.365 r_scbond_it 2.141 r_mcangle_it 1.385 r_angle_refined_deg 1.357 r_mcbond_it 0.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.592 r_dihedral_angle_4_deg 14.32 r_dihedral_angle_3_deg 13.6 r_sphericity_free 8.579 r_dihedral_angle_1_deg 5.883 r_scangle_it 3.365 r_scbond_it 2.141 r_mcangle_it 1.385 r_angle_refined_deg 1.357 r_mcbond_it 0.776 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.249 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.118 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.11 r_metal_ion_refined 0.1 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1019 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 9
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling