☰ Navigation Tabs
X-ray structure of Hen Egg White Lysozyme with dirhodium tetraacetate (2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 193L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 0.1 M sodium acetate, 20% ethylene glicol, 0.6 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 1.98 37.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.948 α = 90 b = 77.948 β = 90 c = 37.38 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 RIGAKU SATURN 944 2016-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.62 26.99 98.7 0.068 0.021 0.999 56.7 9 15018
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.65 86.6 0.19 0.152 0.942 3.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 193l 1.62 26.99 14977 736 98.656 0.166 0.1646 0.173 0.2028 0.2121 21.371
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] -0.263 -0.263 0.525
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.508 r_dihedral_angle_4_deg 14.969 r_dihedral_angle_3_deg 11.544 r_dihedral_angle_1_deg 6.576 r_lrange_it 5.829 r_lrange_other 5.828 r_scangle_it 4.544 r_scangle_other 4.542 r_scbond_it 3.217 r_scbond_other 3.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.508 r_dihedral_angle_4_deg 14.969 r_dihedral_angle_3_deg 11.544 r_dihedral_angle_1_deg 6.576 r_lrange_it 5.829 r_lrange_other 5.828 r_scangle_it 4.544 r_scangle_other 4.542 r_scbond_it 3.217 r_scbond_other 3.215 r_mcangle_other 2.382 r_mcangle_it 2.381 r_angle_refined_deg 1.958 r_mcbond_it 1.841 r_mcbond_other 1.665 r_angle_other_deg 1.645 r_symmetry_xyhbond_nbd_refined 0.286 r_symmetry_nbd_refined 0.282 r_nbd_other 0.277 r_xyhbond_nbd_refined 0.254 r_nbd_refined 0.225 r_symmetry_nbd_other 0.215 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_other 0.164 r_ext_dist_refined_d 0.104 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.087 r_metal_ion_refined 0.062 r_gen_planes_refined 0.02 r_bond_refined_d 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing