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Methionine synthase folate-binding domain with methyltetrahydrofolate from Thermus thermophilus HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VON
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 277 0.1 M sodium citrate pH 4.5, 22 % polyethylene glycol 3350, 0.2 M tri-sodium citrate, soaked with 6S-methyltetrahydrofolate
Crystal Properties Matthews coefficient Solvent content 3.2 61.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.463 α = 90 b = 188.463 β = 90 c = 247.137 γ = 120
Symmetry Space Group P 61 2 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 EIGER X 16M 2016-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 163.21 99.4 0.092 0.048 0.996 8.93 4.5 100615
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 98.4 0.645 0.342 0.651 1.92 4.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5VON 2.4 163.21 95477 5056 99.29 0.19235 0.19039 0.1917 0.22972 0.231 RANDOM 50.272
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] 0.35 0.18 0.35 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.384 r_dihedral_angle_4_deg 16.284 r_dihedral_angle_3_deg 13.683 r_long_range_B_other 6.264 r_long_range_B_refined 6.262 r_dihedral_angle_1_deg 6.043 r_scangle_other 4.526 r_mcangle_it 3.726 r_mcangle_other 3.726 r_scbond_it 2.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.384 r_dihedral_angle_4_deg 16.284 r_dihedral_angle_3_deg 13.683 r_long_range_B_other 6.264 r_long_range_B_refined 6.262 r_dihedral_angle_1_deg 6.043 r_scangle_other 4.526 r_mcangle_it 3.726 r_mcangle_other 3.726 r_scbond_it 2.687 r_scbond_other 2.687 r_mcbond_it 2.329 r_mcbond_other 2.327 r_angle_refined_deg 1.363 r_angle_other_deg 0.917 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13257 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 232
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing