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Structure of a pseudomurein peptide ligase type E from Methanothermobacter thermautotrophicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JT8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM amino acids mix; 0.1 M buffer system 6, pH 8.5; 50% v/v precipitant mix of 25% w/v PEG4000 and 40% w/v 1,2,6-hexanetriol
Crystal Properties Matthews coefficient Solvent content 2.91 57.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.266 α = 90 b = 127.423 β = 90 c = 134.736 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 EIGER X 16M 2017-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.987 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.91 47.24 99.5 0.1 0.99 3.92 13.6 25647 68.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.91 2.94 97 0.834
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7JT8 2.911 46.29 25593 1257 99.5 0.2135 0.2119 0.2466 0.2236 RANDOM 74.98
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] -10.3928 3.9745 6.4183
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.68 t_omega_torsion 2.79 t_angle_deg 1 t_bond_d 0.009 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6825 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing