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Ternary complex structure of leucoanthocyanidin reductase from vitis vinifera
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CJV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 Sodium acetate 0.3M, PEG 4000 32.5%, TRIS HCL 0.1M, Glycerol 2.5%, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 40.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.681 α = 90 b = 50.87 β = 102.71 c = 68.961 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 CCD MARMOSAIC 225 mm CCD Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry 2008-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.28 40.59 93.85 0.08 0.08 7.5 2.4 13391 13391 29.25
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.4 97.5 0.338 0.338 2 2.3 1979
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3cjv 2.28 40.59 13391 12715 675 93.85 0.14537 0.14537 0.14198 0.1603 0.21196 0.2247 RANDOM 11.066
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 -0.19 -0.02 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.929 r_dihedral_angle_4_deg 13.539 r_dihedral_angle_3_deg 12.988 r_dihedral_angle_1_deg 6.314 r_scangle_it 6.144 r_scbond_it 4.49 r_mcangle_it 3.764 r_mcbond_it 2.539 r_angle_other_deg 2.29 r_angle_refined_deg 1.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.929 r_dihedral_angle_4_deg 13.539 r_dihedral_angle_3_deg 12.988 r_dihedral_angle_1_deg 6.314 r_scangle_it 6.144 r_scbond_it 4.49 r_mcangle_it 3.764 r_mcbond_it 2.539 r_angle_other_deg 2.29 r_angle_refined_deg 1.485 r_mcbond_other 0.307 r_chiral_restr 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2275 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 69
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling