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Methionine synthase, C-terminal fragment, Cobalamin and Reactivation Domains from Thermus thermophilus HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BUL Minus Cap Domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277.15 0.1 M Bis-Tris Propane, pH 7, 60% v/v Tacismate, pH 7, 5% PEG 300, 10% ethylene glycol, 1.5 mM cyanocobalamin
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.135 α = 90 b = 95.844 β = 91.956 c = 238.745 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M K-B pair of biomorph mirrors for vertical and horizontal focusing 2022-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
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 3.15 49.295 98.9 0.192 0.228 0.121 0.989 4.6 3.5 64421
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 3.15 3.23 99.4 0.973 1.152 0.609 0.583 3.5
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 (All) 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 3bul 3.15 49.295 64409 3279 98.691 0.248 0.2453 0.2457 0.3067 0.3052 RANDOM 82.81
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] -1.308 -2.874 -0.296 1.796
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 21.946 r_lrange_it 21.943 r_dihedral_angle_6_deg 16.006 r_dihedral_angle_3_deg 15.674 r_scangle_it 13.54 r_scangle_other 13.54 r_mcangle_it 13.224 r_mcangle_other 13.224 r_dihedral_angle_2_deg 11.121 r_scbond_it 8.404
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 21.946 r_lrange_it 21.943 r_dihedral_angle_6_deg 16.006 r_dihedral_angle_3_deg 15.674 r_scangle_it 13.54 r_scangle_other 13.54 r_mcangle_it 13.224 r_mcangle_other 13.224 r_dihedral_angle_2_deg 11.121 r_scbond_it 8.404 r_scbond_other 8.404 r_mcbond_it 8.37 r_mcbond_other 8.369 r_dihedral_angle_1_deg 7.18 r_angle_refined_deg 1.929 r_angle_other_deg 1.019 r_symmetry_xyhbond_nbd_refined 0.162 r_nbd_refined 0.148 r_nbtor_refined 0.148 r_symmetry_nbd_other 0.133 r_nbd_other 0.133 r_symmetry_nbd_refined 0.127 r_chiral_restr_other 0.115 r_xyhbond_nbd_refined 0.111 r_ncsr_local_group_14 0.101 r_ncsr_local_group_5 0.098 r_ncsr_local_group_9 0.098 r_ncsr_local_group_10 0.097 r_ncsr_local_group_12 0.097 r_ncsr_local_group_6 0.096 r_ncsr_local_group_15 0.096 r_ncsr_local_group_1 0.094 r_ncsr_local_group_3 0.094 r_chiral_restr 0.093 r_ncsr_local_group_7 0.093 r_ncsr_local_group_8 0.092 r_ncsr_local_group_2 0.089 r_ncsr_local_group_4 0.089 r_ncsr_local_group_11 0.089 r_ncsr_local_group_13 0.088 r_symmetry_nbtor_other 0.066 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.005 r_symmetry_xyhbond_nbd_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 24040 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 546
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing