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Crystal structure of the cobalamin-independent methionine synthase enzyme in a closed conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L5Z PDB ENTRY 4L5Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 50 mM sodium iodide, 27% w/v PEG3350, 0.25 mM BME, 0.15 mM zinc sulfate, 2 mM homocysteine, 5 mM 5-methyltetrahydrofolate triglutamate, 20 mM Tris-Cl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.978 α = 90 b = 99.102 β = 90 c = 103.902 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 CCD ADSC QUANTUM 315r 2014-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97648 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.98 71.71 100 0.172 5.4 7.8 16415 16414
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.98 3.03 100 0.601
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 4L5Z 2.98 71.71 16415 15543 828 99.93 0.18041 0.17544 0.1785 0.2757 0.2657 RANDOM 31.671
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] -1.19 2.53 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.45 r_dihedral_angle_3_deg 16.551 r_dihedral_angle_4_deg 14.594 r_dihedral_angle_1_deg 6.846 r_long_range_B_refined 4.234 r_long_range_B_other 4.234 r_mcangle_other 2.759 r_scangle_other 2.434 r_angle_refined_deg 1.635 r_scbond_other 1.426
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.45 r_dihedral_angle_3_deg 16.551 r_dihedral_angle_4_deg 14.594 r_dihedral_angle_1_deg 6.846 r_long_range_B_refined 4.234 r_long_range_B_other 4.234 r_mcangle_other 2.759 r_scangle_other 2.434 r_angle_refined_deg 1.635 r_scbond_other 1.426 r_mcangle_it 1.303 r_angle_other_deg 0.832 r_mcbond_it 0.762 r_mcbond_other 0.761 r_scbond_it 0.72 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 5888 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 69
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling