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The crystallographic structure of the digestive lysozyme 1 from Musca domestica at 1.90 Ang.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HEW PDB ENTRY 1HEW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 1% PEG 400, 0.1 M Na Hepes, 1.4 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.523 α = 90 b = 79.435 β = 102.97 c = 45.203 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2003-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.4310 LNLS D03B-MX1
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 1.9 40 100 0.052 23.8 3.5 19857 19857
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 1.9 1.97 99.8 0.222 5.6 3.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1HEW 1.9 30 18817 18817 1016 99.97 0.15565 0.15333 0.1584 0.19802 0.1593 RANDOM 28.331
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] 1.26 -0.5 -1.14 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.405 r_dihedral_angle_4_deg 14.691 r_dihedral_angle_3_deg 12.939 r_dihedral_angle_1_deg 6.382 r_scangle_it 2.744 r_scbond_it 1.987 r_angle_refined_deg 1.365 r_mcangle_it 1.141 r_mcbond_it 0.673 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.405 r_dihedral_angle_4_deg 14.691 r_dihedral_angle_3_deg 12.939 r_dihedral_angle_1_deg 6.382 r_scangle_it 2.744 r_scbond_it 1.987 r_angle_refined_deg 1.365 r_mcangle_it 1.141 r_mcbond_it 0.673 r_nbtor_refined 0.314 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.2 r_symmetry_hbond_refined 0.148 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.083 r_bond_refined_d 0.012 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_refined 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 1938 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing