☰ Navigation Tabs
Crystal structure of 1L-myo-inositol 1-phosphate synthase 1 from Oryza sativa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RM0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Magnesium chloride hexahydrate, 0.1M Tris-HCl at pH8.0 and 25% (w/v) Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.31 46.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.301 α = 90 b = 137.079 β = 90 c = 217.966 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 PIXEL DECTRIS EIGER X 4M 2024-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.01200 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.79 49.08 100 0.187 0.993 10.3 7 198484
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.82 100 0.893 0.652 2.1 7.1
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 1.79 47.45 188357 10011 99.98 0.14996 0.14794 0.1607 0.18833 0.1966 RANDOM 14.03
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] 0.01 0.12 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.971 r_dihedral_angle_2_deg 7.929 r_dihedral_angle_1_deg 7.021 r_long_range_B_other 5.469 r_long_range_B_refined 5.468 r_scangle_other 4.396 r_scbond_it 2.998 r_scbond_other 2.998 r_angle_refined_deg 2.175 r_mcangle_it 2.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.971 r_dihedral_angle_2_deg 7.929 r_dihedral_angle_1_deg 7.021 r_long_range_B_other 5.469 r_long_range_B_refined 5.468 r_scangle_other 4.396 r_scbond_it 2.998 r_scbond_other 2.998 r_angle_refined_deg 2.175 r_mcangle_it 2.022 r_mcangle_other 2.022 r_mcbond_it 1.467 r_mcbond_other 1.467 r_angle_other_deg 0.732 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 15686 Nucleic Acid Atoms Solvent Atoms 1657 Heterogen Atoms 352
Software Software Software Name Purpose REFMAC refinement BUCCANEER model building Coot model building MOLREP phasing XDS data reduction XDS data scaling