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Crystal structure of gamma-Glutamyl-Methylamide Synthetase from Methylovorus mays (MmGmaS) in complex with ATPgS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold model of MmGmaS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.03M Magnesium chloride hexahydrate, 0.03M Calcium chloride dihydrate, 20% v/v Ethylene glycol, 10 % w/v PEG 8000, 0.1 M Imidazole, 0.1 M MES monohydrate, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.92 57.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.74 α = 90 b = 246.923 β = 111.17 c = 105.76 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 R 4M 2024-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 2.65 90.89 98.7 0.9 4.2 6.1 97024
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.7 0.354 0.9
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 2.65 90.89 94983 2031 98.68 0.22552 0.22478 0.25968 0.2434 RANDOM 37.849
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] 0.03 0.11 -0.14 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.116 r_dihedral_angle_3_deg 13.04 r_long_range_B_refined 7.658 r_dihedral_angle_1_deg 6.396 r_mcangle_it 4.107 r_scbond_it 3.054 r_mcbond_it 2.526 r_angle_refined_deg 1.435 r_chiral_restr 0.096 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.116 r_dihedral_angle_3_deg 13.04 r_long_range_B_refined 7.658 r_dihedral_angle_1_deg 6.396 r_mcangle_it 4.107 r_scbond_it 3.054 r_mcbond_it 2.526 r_angle_refined_deg 1.435 r_chiral_restr 0.096 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 20722 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 204
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing