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Crystal structure of Os79 T291V from O. sativa in complex with UDP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 50 mM HEPES pH 7.5, 32% MEPEG 5K
Crystal Properties Matthews coefficient Solvent content 2.52 51.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.462 α = 90 b = 83.219 β = 90 c = 98.67 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 CCD ADSC QUANTUM 210r 2016-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.979 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.58 50 99.8 83.6 8.4 63979
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 5tme 1.58 50 63979 3395 99.58 0.16617 0.16457 0.1787 0.1966 0.2107 RANDOM 27.877
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.483 r_dihedral_angle_4_deg 15.235 r_dihedral_angle_3_deg 13.45 r_long_range_B_other 7.257 r_long_range_B_refined 7.248 r_dihedral_angle_1_deg 6.199 r_scangle_other 5.938 r_scbond_it 4.345 r_scbond_other 4.293 r_mcangle_other 3.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.483 r_dihedral_angle_4_deg 15.235 r_dihedral_angle_3_deg 13.45 r_long_range_B_other 7.257 r_long_range_B_refined 7.248 r_dihedral_angle_1_deg 6.199 r_scangle_other 5.938 r_scbond_it 4.345 r_scbond_other 4.293 r_mcangle_other 3.382 r_mcangle_it 3.381 r_angle_refined_deg 2.504 r_mcbond_it 2.475 r_mcbond_other 2.469 r_angle_other_deg 1.123 r_chiral_restr 0.175 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3407 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 phasing