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Crystal structure of rice DWARF14 (D14)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IH1
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 2.2 44.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.196 α = 90 b = 88.46 β = 90 c = 121.228 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) 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 40 99.7 76211 76002 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 4IH1 1.55 40 2 75984 5487 99.98 0.1802 0.1789 0.1889 0.197 0.205 RANDOM 15.7356
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] -0.02 0.06 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.645 r_dihedral_angle_4_deg 15.36 r_dihedral_angle_3_deg 12.009 r_dihedral_angle_1_deg 4.829 r_scangle_it 4.041 r_scbond_it 2.498 r_mcangle_it 1.647 r_angle_refined_deg 1.235 r_mcbond_it 0.853 r_angle_other_deg 0.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.645 r_dihedral_angle_4_deg 15.36 r_dihedral_angle_3_deg 12.009 r_dihedral_angle_1_deg 4.829 r_scangle_it 4.041 r_scbond_it 2.498 r_mcangle_it 1.647 r_angle_refined_deg 1.235 r_mcbond_it 0.853 r_angle_other_deg 0.847 r_mcbond_other 0.21 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4100 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling