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Grimophan Synthase from Variovorax boronicumulans (GriS): open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 293 1 M Na/K-phosphate
Crystal Properties Matthews coefficient Solvent content 4.61 73.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.36 α = 90 b = 79.36 β = 90 c = 183.97 γ = 120
Symmetry Space Group P 32 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 2026-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9184 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.4 30 99.9 0.096 11.3 10.2 27004
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 2.4 2.5 99.6 0.842 2.5 10.5
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 2.4 30 25636 1350 99.79 0.19352 0.19257 0.1916 0.23417 0.2377 RANDOM 78.444
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 0.5 1 -3.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.638 r_dihedral_angle_4_deg 19.821 r_dihedral_angle_3_deg 15.306 r_long_range_B_refined 8.727 r_long_range_B_other 8.679 r_scangle_other 7.641 r_mcangle_it 6.547 r_mcangle_other 6.547 r_scbond_it 5.753 r_scbond_other 5.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.638 r_dihedral_angle_4_deg 19.821 r_dihedral_angle_3_deg 15.306 r_long_range_B_refined 8.727 r_long_range_B_other 8.679 r_scangle_other 7.641 r_mcangle_it 6.547 r_mcangle_other 6.547 r_scbond_it 5.753 r_scbond_other 5.751 r_dihedral_angle_1_deg 5.341 r_mcbond_it 4.935 r_mcbond_other 4.919 r_angle_other_deg 1.13 r_angle_refined_deg 1.126 r_rigid_bond_restr 0.88 r_chiral_restr 0.05 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2344 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing