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Crystal structure of hen egg white lysozyme soaked with 100mM RhCl3 at pH3.8
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 1.98 37.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.956 α = 90 b = 77.956 β = 90 c = 37.305 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 2009-02-05 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 1.5 80 99.9 0.063 24.4 18981 18.672
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) 1.5 1.55 100 0.319 25.2
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 1.5 20.57 17962 975 99.86 0.20237 0.20035 0.1981 0.24292 0.2425 RANDOM 17.627
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 32.49 r_dihedral_angle_4_deg 15.589 r_dihedral_angle_3_deg 11.651 r_sphericity_free 10.783 r_dihedral_angle_1_deg 5.558 r_scangle_it 2.92 r_scbond_it 1.914 r_mcangle_it 1.26 r_angle_refined_deg 1.229 r_mcbond_it 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.49 r_dihedral_angle_4_deg 15.589 r_dihedral_angle_3_deg 11.651 r_sphericity_free 10.783 r_dihedral_angle_1_deg 5.558 r_scangle_it 2.92 r_scbond_it 1.914 r_mcangle_it 1.26 r_angle_refined_deg 1.229 r_mcbond_it 0.69 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.246 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.095 r_metal_ion_refined 0.03 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1013 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 10
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling