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T4 lysozyme mutant L99A in complex with 3-butylpyridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4W57
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 Isopropanol, PEG 4000, Tris-Cl pH 8.0, Beta-mercaptoethanol, 2-hyrdoxyethyl disulfide
Crystal Properties Matthews coefficient Solvent content 2.56 51.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.248 α = 90 b = 60.248 β = 90 c = 96.119 γ = 120
Symmetry Space Group P 32 2 1
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 S 6M 2020-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 0.9539 ALS 8.3.1
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 0.99 52.18 96.6 0.036 0.037 0.009 1 30.2 16.5 108816 11.96
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 0.99 1.01 69.1 0.862 0.963 0.414 0.724 5
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 THROUGHOUT 4W57 0.99 52.176 1.34 108714 5610 96.47 0.1976 0.1975 0.2003 0.1996 0.2015 13.7836
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 3.489 f_angle_d 0.774 f_chiral_restr 0.065 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1277 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction