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Structure of BT1526, a myo-inositol-1-phosphate synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 200 mM Sodium Formate 100 mM Bis Tris propane pH 6.5 20 % (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.14 42.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.805 α = 90 b = 104.563 β = 90 c = 124.318 γ = 90
Symmetry Space Group P 2 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 EIGER2 XE 16M 2020-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9796 Diamond I04
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 58.85 100 0.998 11.2 13.3 59644
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 2.05 0.541 13.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3QVT 2 58.847 59567 2989 99.963 0.185 0.183 0.183 0.2252 0.2253 34.103
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] -0.185 0.145 0.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.994 r_dihedral_angle_4_deg 19.07 r_dihedral_angle_3_deg 14.903 r_dihedral_angle_1_deg 6.39 r_lrange_it 6.167 r_scangle_it 5.078 r_scbond_it 3.667 r_mcangle_it 3.394 r_mcbond_it 2.541 r_angle_refined_deg 1.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.994 r_dihedral_angle_4_deg 19.07 r_dihedral_angle_3_deg 14.903 r_dihedral_angle_1_deg 6.39 r_lrange_it 6.167 r_scangle_it 5.078 r_scbond_it 3.667 r_mcangle_it 3.394 r_mcbond_it 2.541 r_angle_refined_deg 1.407 r_nbtor_refined 0.312 r_symmetry_nbd_refined 0.236 r_symmetry_xyhbond_nbd_refined 0.216 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.096 r_ncsr_local_group_1 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6738 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction xia2 data reduction PHASER phasing Coot model building