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Crystal Structure of Canine Milk Lysozyme Stabilized against Non-enzymatic Deamidation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CWI PDB ENTRY 2CWI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 10mM sodium citrate, 1M ammonium sulfate, 5% ethylene glycol, 2.5% iso-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.92 35.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.216 α = 90 b = 31.216 β = 90 c = 198.307 γ = 120
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++ 2006-08-18 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 2.01 50 97.9 25.927 14424 14193 20.023
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.01 2.08 11.992
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 2CWI 2.01 27.04 12996 682 95.48 0.2795 0.27264 0.2611 0.41266 0.3971 RANDOM 15.382
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] -0.09 -0.05 -0.09 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.94 r_dihedral_angle_3_deg 22.279 r_dihedral_angle_4_deg 16.091 r_dihedral_angle_1_deg 10.916 r_scangle_it 4.774 r_scbond_it 3.66 r_angle_refined_deg 2.774 r_mcangle_it 2.021 r_mcbond_it 1.368 r_symmetry_hbond_refined 0.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.94 r_dihedral_angle_3_deg 22.279 r_dihedral_angle_4_deg 16.091 r_dihedral_angle_1_deg 10.916 r_scangle_it 4.774 r_scbond_it 3.66 r_angle_refined_deg 2.774 r_mcangle_it 2.021 r_mcbond_it 1.368 r_symmetry_hbond_refined 0.477 r_symmetry_vdw_refined 0.422 r_xyhbond_nbd_refined 0.395 r_nbtor_refined 0.319 r_nbd_refined 0.3 r_chiral_restr 0.208 r_bond_refined_d 0.032 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2030 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing