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Previously de-ionized HEW lysozyme batch crystallized in 0.5 M YbCl3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 193L PDB ENTRY 193L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 293 Previously de-ionized lysozyme, no buffer added, 0.5 M YbCl3, pH 4.5, Batch crystallization, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 39.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.906 α = 90 b = 78.906 β = 90 c = 37.699 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 295 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2000-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LURE BEAMLINE DW32 LURE DW32
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.64 27.26 99.8 0.067 13 5.1 15095 16.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.7 100 0.298 3.4 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 193L 1.64 55.79 27665 13870 1185 99.68 0.17139 0.17008 0.1723 0.1861 0.1921 RANDOM 21.731
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] 0.22 0.22 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.355 r_dihedral_angle_3_deg 15.65 r_dihedral_angle_4_deg 9.561 r_dihedral_angle_1_deg 5.393 r_scbond_it 3.771 r_mcangle_it 1.855 r_mcbond_it 1.221 r_mcbond_other 1.22 r_angle_refined_deg 1.049 r_angle_other_deg 0.763
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.355 r_dihedral_angle_3_deg 15.65 r_dihedral_angle_4_deg 9.561 r_dihedral_angle_1_deg 5.393 r_scbond_it 3.771 r_mcangle_it 1.855 r_mcbond_it 1.221 r_mcbond_other 1.22 r_angle_refined_deg 1.049 r_angle_other_deg 0.763 r_chiral_restr 0.066 r_bond_refined_d 0.006 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_mcangle_other r_scbond_other r_scangle_it 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 1001 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement AMoRE phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling TRUNCATE data scaling HKL-2000 data collection