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Crystal structure analysis of Hen egg white lysozyme grown by capillary method
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 capillary method 4.7 298 0.04m NAOAC/HOAC buffer, pH 4.7, capillary method, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.07 40.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.243 α = 90 b = 79.243 β = 90 c = 37.829 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 293 IMAGE PLATE RIGAKU M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.5 39.53 4332 1 1 22.02
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) 2.5 39.53 98.5 0.092 5.9 4332
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 2.5 39.53 4189 203 98.5 0.16681 0.16454 0.1733 0.21131 0.2148 RANDOM 22.024
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] 0.05 0.05 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.007 r_scangle_it 7.435 r_scbond_it 4.907 r_dihedral_angle_1_deg 4.459 r_mcangle_it 3.235 r_angle_refined_deg 2.441 r_angle_other_deg 1.964 r_mcbond_it 1.939 r_symmetry_hbond_refined 1.304 r_symmetry_hbond_other 0.575
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.007 r_scangle_it 7.435 r_scbond_it 4.907 r_dihedral_angle_1_deg 4.459 r_mcangle_it 3.235 r_angle_refined_deg 2.441 r_angle_other_deg 1.964 r_mcbond_it 1.939 r_symmetry_hbond_refined 1.304 r_symmetry_hbond_other 0.575 r_symmetry_vdw_refined 0.427 r_symmetry_vdw_other 0.384 r_xyhbond_nbd_other 0.248 r_nbd_refined 0.24 r_nbd_other 0.22 r_chiral_restr 0.175 r_xyhbond_nbd_refined 0.142 r_bond_refined_d 0.037 r_gen_planes_refined 0.017 r_gen_planes_other 0.013 r_bond_other_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection AUTOMAR data reduction AMoRE phasing