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Hen lysozyme in tetragonal space group at ambient temperature - diffuse scattering dataset
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 4.8 295 Reservoir contained 1.1 M NaCl, 0.1 M NaOAc pH 4.8. Drops contained 2 microliters each of 40 mg/mL protein and well solution.
Crystal Properties Matthews coefficient Solvent content 2.12 41.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.632 α = 90 b = 79.632 β = 90 c = 38.296 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 298 PIXEL DECTRIS PILATUS3 6M 100 micron collimator 2017-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.9768 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.27 39.82 98 0.046 0.047 0.009 1 39.2 23.8 32284
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.27 1.29 78.1 0.38 0.426 0.184 0.878 3.7 4.6
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 193L 1.272 39.82 32215 1659 97.885 0.116 0.1149 0.1332 0.1518 25.565
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] 0.198 0.198 -0.396
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.277 r_rigid_bond_restr 30.472 r_scbond_it 29.262 r_scbond_other 29.235 r_dihedral_angle_4_deg 26.665 r_scangle_it 21.924 r_scangle_other 21.911 r_lrange_other 18.149 r_lrange_it 18.109 r_mcbond_it 16.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.277 r_rigid_bond_restr 30.472 r_scbond_it 29.262 r_scbond_other 29.235 r_dihedral_angle_4_deg 26.665 r_scangle_it 21.924 r_scangle_other 21.911 r_lrange_other 18.149 r_lrange_it 18.109 r_mcbond_it 16.227 r_mcbond_other 16.181 r_dihedral_angle_3_deg 11.14 r_mcangle_other 11.017 r_mcangle_it 11.016 r_dihedral_angle_1_deg 6.014 r_angle_refined_deg 2.054 r_angle_other_deg 1.599 r_nbd_refined 0.23 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.169 r_nbd_other 0.159 r_chiral_restr 0.131 r_xyhbond_nbd_refined 0.12 r_symmetry_nbtor_other 0.086 r_metal_ion_refined 0.058 r_symmetry_xyhbond_nbd_refined 0.033 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.008 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1000 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Aimless data scaling Coot model building XDS data reduction REFMAC phasing