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Crystal Structure of Human Lysozyme from Urine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I1Z PDB ENTRY 1I1Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 2.5M sodium chloride, 0.03M phosphate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2 38.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.7 α = 90 b = 61 β = 90 c = 34 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 277 IMAGE PLATE RIGAKU RAXIS IIC double-mirror 2002-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 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 1.8 41.52 91.2 0.084 29167 11190
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 1I1Z 1.8 41.52 9926 504 91.24 0.17305 0.17035 0.1715 0.22671 0.1863 RANDOM 13.497
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] 0.06 0.01 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.629 r_dihedral_angle_4_deg 15.029 r_dihedral_angle_3_deg 13.256 r_dihedral_angle_1_deg 6.149 r_scangle_it 4.364 r_scbond_it 2.627 r_angle_refined_deg 1.411 r_mcangle_it 1.348 r_mcbond_it 0.767 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.629 r_dihedral_angle_4_deg 15.029 r_dihedral_angle_3_deg 13.256 r_dihedral_angle_1_deg 6.149 r_scangle_it 4.364 r_scbond_it 2.627 r_angle_refined_deg 1.411 r_mcangle_it 1.348 r_mcbond_it 0.767 r_nbtor_refined 0.297 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.15 r_metal_ion_refined 0.148 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.108 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1029 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing