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Structure of Epimerase Mth373 from the thermophilic pseudomurein-containing methanogen Methanothermobacter thermautotrophicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KEW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 294 0.2 M MgCl2, 0.1 M sodium citrate tribasic dihydrate, 10% w/v polyethylene glycol (PEG) 20,000
Crystal Properties Matthews coefficient Solvent content 2.29 41.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.481 α = 90 b = 81.38 β = 90 c = 152.39 γ = 90
Symmetry Space Group P 2 2 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 CCD ADSC QUANTUM 210r 2017-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95370 Australian Synchrotron MX1
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 2 45.27 99.8 0.192 0.207 0.076 0.994 9.4 7.3 46865
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 2 2.05 98 0.768 0.827 0.304 0.796 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 45.27 44537 2289 99.85 0.16546 0.16347 0.20391 0.1752 RANDOM 17.005
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] 0.98 -0.44 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.201 r_dihedral_angle_4_deg 18.887 r_dihedral_angle_3_deg 14.276 r_dihedral_angle_1_deg 6.545 r_long_range_B_refined 4.472 r_mcangle_it 1.667 r_angle_refined_deg 1.533 r_scbond_it 1.465 r_mcbond_it 0.997 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.201 r_dihedral_angle_4_deg 18.887 r_dihedral_angle_3_deg 14.276 r_dihedral_angle_1_deg 6.545 r_long_range_B_refined 4.472 r_mcangle_it 1.667 r_angle_refined_deg 1.533 r_scbond_it 1.465 r_mcbond_it 0.997 r_chiral_restr 0.1 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5169 Nucleic Acid Atoms Solvent Atoms 433 Heterogen Atoms 187
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing