☰ Navigation Tabs
Crystal structure of Hen egg-white lysozyme in Tris buffer at pH 7.5 with Magnesium formate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2LYZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 80mg/ml hen egg-white lysozyme, 100mM TrisHCl, 0.4M Mg-Formate(0.2~0.6 M), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.9 35.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.594 α = 90 b = 76.594 β = 90 c = 37.065 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 2013-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6C1 PAL/PLS 6C1
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 1.34 50 99.8 0.137 0.137 59.724 11.1 349012 349012 -3
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 1.34 1.36 99.7 0.536 0.536 1.6
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 2LYZ 1.34 38.3 24101 1290 99.63 0.16967 0.16718 0.1767 0.21821 0.2325 RANDOM 19.282
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] -11.21 -11.21 22.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.396 r_sphericity_free 30.514 r_dihedral_angle_4_deg 17.226 r_sphericity_bonded 15.632 r_dihedral_angle_3_deg 14.265 r_dihedral_angle_1_deg 6.012 r_rigid_bond_restr 5.634 r_angle_refined_deg 2.04 r_angle_other_deg 1.184 r_chiral_restr 0.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.396 r_sphericity_free 30.514 r_dihedral_angle_4_deg 17.226 r_sphericity_bonded 15.632 r_dihedral_angle_3_deg 14.265 r_dihedral_angle_1_deg 6.012 r_rigid_bond_restr 5.634 r_angle_refined_deg 2.04 r_angle_other_deg 1.184 r_chiral_restr 0.149 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1000 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling