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Crystal Structure Analysis of Hexagonal Lysozyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DPW 1DPW.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.4 293 10% aqu. acetone solution saturated with sodium nitrate, 25mg/ml lysozyme, pH 8.4, batch, temperature 293.0K, pH 8.40
Crystal Properties Matthews coefficient Solvent content 2.51 50.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.637 α = 90 b = 85.637 β = 90 c = 67.932 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 10 CCD MARRESEARCH 2004-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 1.46 70 100 0.038 77.6 23 25570 3.5
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 1.46 1.47 100 0.884 3.5 13.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1DPW.pdb 1.46 70 26041 25016 528 98.1 0.183 0.183 0.198 RANDOM 27.21
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] -0.14 -0.07 -0.14 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.347 r_dihedral_angle_4_deg 17.941 r_dihedral_angle_3_deg 13.55 r_dihedral_angle_1_deg 11.106 r_scangle_it 4.01 r_scbond_it 2.622 r_angle_refined_deg 1.98 r_mcangle_it 1.727 r_mcbond_it 1.419 r_angle_other_deg 1.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.347 r_dihedral_angle_4_deg 17.941 r_dihedral_angle_3_deg 13.55 r_dihedral_angle_1_deg 11.106 r_scangle_it 4.01 r_scbond_it 2.622 r_angle_refined_deg 1.98 r_mcangle_it 1.727 r_mcbond_it 1.419 r_angle_other_deg 1.027 r_symmetry_vdw_refined 0.527 r_mcbond_other 0.389 r_symmetry_hbond_refined 0.344 r_symmetry_vdw_other 0.311 r_xyhbond_nbd_refined 0.303 r_nbd_refined 0.249 r_symmetry_metal_ion_refined 0.211 r_nbd_other 0.204 r_nbtor_refined 0.189 r_metal_ion_refined 0.169 r_chiral_restr 0.133 r_nbtor_other 0.09 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing