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Adenylation domain of the initiation module of LgrA mutant P483M
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ES6 PDB entry 5ES6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 2.37 M sodium formate, 0.112 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 5.93 79.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.18 α = 90 b = 161.18 β = 90 c = 138.63 γ = 90
Symmetry Space Group P 41 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 PILATUS 6M 2019-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97857 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.1 138.6 100 0.019 0.996 24.3 25.6 33772 58.92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.25 99 0.087 0.99 7.6 26.5
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 FOURIER SYNTHESIS FREE R-VALUE PDB entry 5ES6 3.1 113.97 1.35 33695 1687 99.95 0.2133 0.2115 0.2097 0.2464 0.2429 54.67
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 6.6043 f_angle_d 0.5072 f_chiral_restr 0.0432 f_bond_d 0.0025 f_plane_restr 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4655 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling