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Previously de-ionized HEW lysozyme crystallized in 0.5 M YbCl3/30% (v/v) glycerol and collected at 125K
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, 30% (v/v) glycerol , pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.589 α = 90 b = 78.589 β = 90 c = 37.017 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 125 IMAGE PLATE RIGAKU RAXIS IIC 2000-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 1.7 19.65 99.7 0.067 23.3 9.4 13242 20.1
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 1.7 1.76 97.7 0.202 3.8 4.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 193L 1.7 55.57 21872 11957 1241 99.51 0.18081 0.17824 0.20515 0.2529 RANDOM 21.581
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] 0.51 0.51 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.818 r_dihedral_angle_4_deg 17.71 r_dihedral_angle_3_deg 13.763 r_dihedral_angle_1_deg 5.379 r_scbond_it 3.38 r_mcangle_it 1.907 r_mcbond_it 1.374 r_mcbond_other 1.318 r_angle_refined_deg 1.296 r_angle_other_deg 0.861
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.818 r_dihedral_angle_4_deg 17.71 r_dihedral_angle_3_deg 13.763 r_dihedral_angle_1_deg 5.379 r_scbond_it 3.38 r_mcangle_it 1.907 r_mcbond_it 1.374 r_mcbond_other 1.318 r_angle_refined_deg 1.296 r_angle_other_deg 0.861 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 129 Heterogen Atoms 6
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