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Dialyzed HEW lysozyme batch crystallized in 0.5 M YbCl3 and collected at 100 K
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 Dialyzed lysozyme, no buffer added, 0.5 M YbCl3, pH 4.5, Batch crystallization, EVAPORATION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.665 α = 90 b = 78.665 β = 90 c = 37.129 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 PIXEL DECTRIS PILATUS 6M MIRRORS 2013-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.37 99.4935 99 0.051 14.1 3.4 46325 15.4
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 1.37 1.45 97.4 0.294 3.48 3.1
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 1.37 55.62 44465 22474 2409 99.24 0.16495 0.1625 0.1691 0.18766 0.1949 RANDOM 19.299
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] -0.07 -0.07 0.15
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.629 r_dihedral_angle_2_deg 35.036 r_dihedral_angle_4_deg 17.658 r_dihedral_angle_3_deg 13.519 r_sphericity_bonded 9.297 r_dihedral_angle_1_deg 5.5 r_rigid_bond_restr 2.219 r_scbond_it 1.956 r_mcangle_it 1.801 r_mcbond_it 1.41
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.629 r_dihedral_angle_2_deg 35.036 r_dihedral_angle_4_deg 17.658 r_dihedral_angle_3_deg 13.519 r_sphericity_bonded 9.297 r_dihedral_angle_1_deg 5.5 r_rigid_bond_restr 2.219 r_scbond_it 1.956 r_mcangle_it 1.801 r_mcbond_it 1.41 r_angle_refined_deg 1.31 r_mcbond_other 1.268 r_angle_other_deg 0.854 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PHASER phasing CNS refinement XDS data reduction XDS data scaling TRUNCATE data scaling MxCuBE data collection