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The crystallographic structure of the digestive lysozyme 2 from Musca domestica at 1.9 Ang.
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 4.2 291 The 3 uL drop was formed by 1.5 uL of protein solution at 9.8 mg/mL in 10 mM MES pH 5.5 plus 1.3 uL of 28% 2-propanol, 0.115 M sodium citrate pH 4.2 and 21% PEG 4000 plus 0.2 uL of 0.2 M ammonium acetate, 0.1 M sodium citrate pH 5.6 and 30% MPD., VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.07 40.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.903 α = 90 b = 96.4 β = 90 c = 33.27 γ = 90
Symmetry Space Group P 21 21 2
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 mirrors 2006-03-20 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 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 30 90.7 0.089 14.4 3.9 17698 17698 23.3
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 74.1 0.304 2.1 1.8 1423
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 (All) 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 2fbd 1.9 30 17674 17674 910 95.9 0.18732 0.18732 0.18355 0.1889 0.25789 0.2646 RANDOM 40.144
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] -1.67 -3.92 5.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.259 r_dihedral_angle_4_deg 17.912 r_dihedral_angle_3_deg 15.428 r_dihedral_angle_1_deg 7.553 r_scangle_it 2.745 r_scbond_it 1.949 r_angle_refined_deg 1.664 r_mcangle_it 1.071 r_mcbond_it 0.668 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.259 r_dihedral_angle_4_deg 17.912 r_dihedral_angle_3_deg 15.428 r_dihedral_angle_1_deg 7.553 r_scangle_it 2.745 r_scbond_it 1.949 r_angle_refined_deg 1.664 r_mcangle_it 1.071 r_mcbond_it 0.668 r_nbtor_refined 0.321 r_nbd_refined 0.228 r_symmetry_hbond_refined 0.193 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.105 r_bond_refined_d 0.017 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 2006 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing