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Structure of N59D HEN EGG-WHITE LYSOZYME in complex with (GlcNAc)3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LZA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.7 293 10% sodium chloride, 0.1M sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.71 α = 90 b = 78.71 β = 90 c = 38.61 γ = 90
Symmetry Space Group P 43 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 281 IMAGE PLATE MAC Science DIP-320 1995-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE MACSCIENCE 1.54
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 2 50 76.6 0.098 3.9 10021 6611
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 1LZA 2 50 5982 629 76.65 0.21284 0.20507 0.2083 0.28656 0.2908 RANDOM 8.63
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] -0.15 -0.15 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.6 r_dihedral_angle_4_deg 15.396 r_dihedral_angle_3_deg 13.876 r_dihedral_angle_1_deg 6.072 r_scangle_it 2.164 r_scbond_it 1.38 r_angle_refined_deg 1.339 r_angle_other_deg 0.971 r_mcangle_it 0.969 r_mcbond_it 0.534
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.6 r_dihedral_angle_4_deg 15.396 r_dihedral_angle_3_deg 13.876 r_dihedral_angle_1_deg 6.072 r_scangle_it 2.164 r_scbond_it 1.38 r_angle_refined_deg 1.339 r_angle_other_deg 0.971 r_mcangle_it 0.969 r_mcbond_it 0.534 r_mcbond_other 0.108 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined 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 96 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement WELMS data collection PROTEIN data reduction PROTEIN data scaling REFMAC phasing