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Structure of D48A hen egg white lysozyme in complex with (GlcNAc)4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LZC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 293 0.1M Sodium acetate buffer, 1.2M NaCl, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.219 α = 90 b = 77.219 β = 90 c = 38.273 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 100 CCD ADSC QUANTUM 270 2010-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A Photon Factory AR-NE3A
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 1.56 50 17024 20.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 50
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 1LZC 1.56 31.34 15330 823 95.1 0.2 0.198 0.1888 0.243 0.2034 RANDOM 13.29
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.994 r_dihedral_angle_4_deg 15.042 r_dihedral_angle_3_deg 13.025 r_dihedral_angle_1_deg 6.79 r_scangle_it 4.521 r_scbond_it 3.068 r_angle_refined_deg 2.258 r_mcangle_it 2.038 r_mcbond_it 1.348 r_chiral_restr 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.994 r_dihedral_angle_4_deg 15.042 r_dihedral_angle_3_deg 13.025 r_dihedral_angle_1_deg 6.79 r_scangle_it 4.521 r_scbond_it 3.068 r_angle_refined_deg 2.258 r_mcangle_it 2.038 r_mcbond_it 1.348 r_chiral_restr 0.311 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 997 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 57
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling