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Crystallographic structure of digestive lysozyme 1 from Musca domestica bound to chitotetraose at 1.92 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FBD PDB ENTRY 2FBD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 1% PEG 400, 0.1M sodium Hepes, 1.4M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.24 45.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.953 α = 90 b = 78.809 β = 102.16 c = 44.792 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 MAR CCD 165 mm mirror 2006-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.427 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.92 30 88.1 0.078 16.2 3.8 16455 16455
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.99 82 0.307 2.4 2.8
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2FBD 1.92 30 15980 15152 828 85.57 0.17843 0.17483 0.24247 0.2335 RANDOM 36.122
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] 1.19 -0.62 -1.83 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.484 r_dihedral_angle_4_deg 19.561 r_dihedral_angle_3_deg 12.894 r_dihedral_angle_1_deg 6.763 r_scangle_it 3.235 r_scbond_it 2.395 r_angle_refined_deg 1.66 r_mcangle_it 1.476 r_mcbond_it 0.884 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.484 r_dihedral_angle_4_deg 19.561 r_dihedral_angle_3_deg 12.894 r_dihedral_angle_1_deg 6.763 r_scangle_it 3.235 r_scbond_it 2.395 r_angle_refined_deg 1.66 r_mcangle_it 1.476 r_mcbond_it 0.884 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.243 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.128 r_chiral_restr 0.107 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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 1937 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data scaling MOLREP phasing