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Crystal structure of rice DWARF14 (D14) in complex with a GR24 hydrolysis intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WOM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 298 PEG6000, MPD, pH 7.5, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.188 α = 90 b = 88.729 β = 90 c = 118.315 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 315r 2011-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.00 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.55 30 99.9 0.107 5 6.6 110233 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.76 99.8 0.779 6.4 10931
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 1WOM 1.55 30 74248 5376 99.76 0.1827 0.1813 0.1892 0.2011 0.2089 RANDOM 20.4594
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] 0.23 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.997 r_dihedral_angle_4_deg 14.71 r_dihedral_angle_3_deg 12.446 r_dihedral_angle_1_deg 5.119 r_scangle_it 4.643 r_scbond_it 2.867 r_mcangle_it 1.964 r_angle_refined_deg 1.461 r_mcbond_it 1.069 r_angle_other_deg 0.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.997 r_dihedral_angle_4_deg 14.71 r_dihedral_angle_3_deg 12.446 r_dihedral_angle_1_deg 5.119 r_scangle_it 4.643 r_scbond_it 2.867 r_mcangle_it 1.964 r_angle_refined_deg 1.461 r_mcbond_it 1.069 r_angle_other_deg 0.892 r_mcbond_other 0.289 r_chiral_restr 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4136 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 18
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction