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High resolution X-ray analysis of ATP lysozyme complex in the presence of 80 mM ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2LZT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 10 mM Tris-HCl pH 7.0, 80 mM Na2-ATP
Crystal Properties Matthews coefficient Solvent content 2.04 39.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.389 α = 90 b = 78.389 β = 90 c = 38.114 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 EIGER2 XE 16M 2020-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.98 Diamond I03
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 39.19 99.99 0.0516 0.05213 0.007296 1 50.22 51.6 31931 12.22
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 1.315 100 0.2322 0.2346 0.03279 0.993 10.3 50.9
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 2LZT 1.27 39.19 1.49 31930 2000 99.99 0.1415 0.1395 0.1401 0.1713 0.1721 20.96
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 8.6749 f_angle_d 1.0881 f_chiral_restr 0.0999 f_plane_restr 0.0106 f_bond_d 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 93
Software Software Software Name Purpose PHENIX refinement PHENIX refinement xia2 data reduction PHASER phasing xia2 data scaling