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M. acetivorans MCR containing a 2-methylglutamine modification
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8GF5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 282.15 25% w/v PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.2 M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 1.95 36.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.47 α = 90 b = 82.94 β = 93.78 c = 122.47 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 X 16M 2023-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE 7B2 0.97 CHESS 7B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 99.5 0.994 8.9 4.7 147424
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 99.9 0.673 0.828 2.89
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 25 140019 7370 99.66 0.15416 0.15213 0.1523 0.19272 0.1925 RANDOM 26.73
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] 1.22 0.17 -2.16 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.087 r_dihedral_angle_2_deg 7.136 r_dihedral_angle_1_deg 6.598 r_long_range_B_refined 4.318 r_scbond_it 1.996 r_mcangle_it 1.762 r_angle_refined_deg 1.648 r_mcbond_it 1.196 r_chiral_restr 0.122 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.087 r_dihedral_angle_2_deg 7.136 r_dihedral_angle_1_deg 6.598 r_long_range_B_refined 4.318 r_scbond_it 1.996 r_mcangle_it 1.762 r_angle_refined_deg 1.648 r_mcbond_it 1.196 r_chiral_restr 0.122 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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 18834 Nucleic Acid Atoms Solvent Atoms 1383 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement autoPROC data processing PHASER phasing XDS data reduction Aimless data scaling