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X-ray Crystal Structure of Bovine Stomach Lysozyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LZ1 PDB ENTRY 1LZ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.94 36.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.257 α = 90 b = 56.065 β = 90 c = 64.05 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 IMAGE PLATE RIGAKU RAXIS IV++ 2006-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 1.5 50 95 36.374 18772 17833 13.074
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.55 17.272
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 1LZ1 1.5 17.94 16849 910 95.1 0.18 0.178 0.1751 0.221 0.1753 RANDOM 13.088
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] 0.11 -0.12 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.141 r_dihedral_angle_4_deg 12.825 r_dihedral_angle_3_deg 10.531 r_dihedral_angle_1_deg 6.033 r_scangle_it 2.495 r_scbond_it 1.66 r_angle_refined_deg 1.261 r_mcangle_it 1.114 r_mcbond_it 0.588 r_chiral_restr 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.141 r_dihedral_angle_4_deg 12.825 r_dihedral_angle_3_deg 10.531 r_dihedral_angle_1_deg 6.033 r_scangle_it 2.495 r_scbond_it 1.66 r_angle_refined_deg 1.261 r_mcangle_it 1.114 r_mcbond_it 0.588 r_chiral_restr 0.332 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.238 r_symmetry_hbond_refined 0.231 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.157 r_metal_ion_refomed 0.101 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1045 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing