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Crystal Structure of Tapes japonica Lysozyme
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 295 0.8M sodium citrate, 0.8M ammonium sulfate, 0.5mM beta-heptyl thioglucoside, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.65 53.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.749 α = 90 b = 88.76 β = 116.04 c = 43.644 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 RIGAKU JUPITER 210 2004-12-04 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD BRUKER SMART 6000 2004-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.97904 SPring-8 BL38B1 2 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1,2 1.6 50 94.8 0.062 0.055 9.4 3.5 38390 36411 63.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.6 1.66 78.4 0.308 0.27 2.3 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MIR THROUGHOUT 1.6 33.86 36384 34538 1836 94.82 0.1764 0.17468 0.1745 0.20994 0.2097 RANDOM 22.18
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.029 r_dihedral_angle_4_deg 12.17 r_dihedral_angle_3_deg 11.822 r_sphericity_free 6.712 r_dihedral_angle_1_deg 4.887 r_scangle_it 1.895 r_scbond_it 1.169 r_angle_refined_deg 1.082 r_mcangle_it 0.856 r_mcbond_it 0.516
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.029 r_dihedral_angle_4_deg 12.17 r_dihedral_angle_3_deg 11.822 r_sphericity_free 6.712 r_dihedral_angle_1_deg 4.887 r_scangle_it 1.895 r_scbond_it 1.169 r_angle_refined_deg 1.082 r_mcangle_it 0.856 r_mcbond_it 0.516 r_nbtor_refined 0.3 r_metal_ion_refined 0.198 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.183 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.093 r_chiral_restr 0.077 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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_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_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1908 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 118
Software Software Software Name Purpose CrystalClear data collection HKL-2000 data reduction SOLVE phasing CNS refinement CrystalClear data reduction HKL-2000 data scaling REFMAC refinement