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Crystal structure of Os79 Q202A 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 7.5 277 100 mM 3-(N- Morpholino)propanesulfonic acid pH 7.5, 15% methyl ether polyethylene glycol 5000 (MEPEG 5K), 160 mM potassium glutamate
Crystal Properties Matthews coefficient Solvent content 2.4 48.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.409 α = 90 b = 83.233 β = 90 c = 99.098 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 PILATUS3 X 6M 2016-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
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 1.47 50 99.2 41.3 13.1 79234
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 1.47 43.46 79234 4150 99.84 0.15408 0.15267 0.1525 0.18068 0.1805 RANDOM 19.157
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 36.076 r_dihedral_angle_3_deg 12.529 r_dihedral_angle_4_deg 12.46 r_long_range_B_refined 7.087 r_long_range_B_other 6.846 r_dihedral_angle_1_deg 6.712 r_scangle_other 5.144 r_scbond_other 3.555 r_scbond_it 3.554 r_mcangle_other 3.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.076 r_dihedral_angle_3_deg 12.529 r_dihedral_angle_4_deg 12.46 r_long_range_B_refined 7.087 r_long_range_B_other 6.846 r_dihedral_angle_1_deg 6.712 r_scangle_other 5.144 r_scbond_other 3.555 r_scbond_it 3.554 r_mcangle_other 3.124 r_mcangle_it 3.122 r_angle_refined_deg 2.874 r_mcbond_it 2.111 r_mcbond_other 2.105 r_angle_other_deg 1.119 r_chiral_restr 0.171 r_bond_refined_d 0.041 r_gen_planes_refined 0.014 r_bond_other_d 0.002 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 3429 Nucleic Acid Atoms Solvent Atoms 583 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 phasing