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Crystal structure of the lysozyme in presence of bromophenol blue at pH 6.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F1M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.3 M sodium chloride, 0.1 M imidazole. After growth, and before measurement, these crystals were soaked in the dye solution: saturated bromophenol blue, 0.3 M sodium chloride, 0.1 M imidazole buffer at pH 6.5.
Crystal Properties Matthews coefficient Solvent content 2.12 41.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.719 α = 90 b = 76.559 β = 90 c = 84.076 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2018-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
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 1.38 19.395 97.5 0.1 0.115 0.055 0.99 7.3 3.8 90196 13.3
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 1.38 1.41 97.2 0.397 0.484 0.271 0.797 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6F1M 1.38 19.39 1.91 90196 4572 94.01 0.1928 0.191 0.1968 0.2261 0.1989 17.47
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 25.037 f_angle_d 0.8965 f_chiral_restr 0.0666 f_bond_d 0.0072 f_plane_restr 0.0045
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1992 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 240
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction