☰ Navigation Tabs
Crystal structure of Gossypium hirsutum (Cotton) 5-enol-pyruvyl-shikimate-3-phosphate synthase (EPSPS) in open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PXY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 0.16 M calcium acetate hydrate, 0.08 M sodium cacodylate (pH 6.5), and 14.4% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.82 56.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.855 α = 90 b = 89.942 β = 107.32 c = 116.233 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU HyPix-6000HE 2024-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.2 24.47 99.9 0.07 0.082 0.998 14.1 6.5 79755
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 2.24 0.782 2.2
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 (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 7PXY 2.2 24.47 75646 3993 99.75 0.20349 0.20112 0.2109 0.24769 0.2541 RANDOM 37.285
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] -0.75 0.73 -0.72 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.761 r_dihedral_angle_2_deg 15.426 r_long_range_B_other 7.572 r_long_range_B_refined 7.571 r_dihedral_angle_1_deg 7.266 r_scangle_other 5.788 r_mcangle_it 4.276 r_mcangle_other 4.276 r_scbond_it 3.871 r_scbond_other 3.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.761 r_dihedral_angle_2_deg 15.426 r_long_range_B_other 7.572 r_long_range_B_refined 7.571 r_dihedral_angle_1_deg 7.266 r_scangle_other 5.788 r_mcangle_it 4.276 r_mcangle_other 4.276 r_scbond_it 3.871 r_scbond_other 3.87 r_mcbond_it 2.807 r_mcbond_other 2.807 r_angle_refined_deg 2.435 r_angle_other_deg 0.809 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 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 9894 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction Aimless data scaling MOLREP phasing