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Structure of the apo form of leucoanthocyanidin reductase from vitis vinifera
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I52
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 PEG 4000 35%, sodium acetate 340mM, Tris 0.1M, sodium azide 3mM, glycerol 3.5%, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.421 α = 90 b = 50.715 β = 103.18 c = 68.051 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 2008-10-07 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) 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 2.72 66.23 90 0.107 5 2.5 7546 7546 44
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 2.72 2.87 92.5 0.294 2 2.5 1132
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 3I52 2.72 66.23 7060 7060 350 89.74 0.17426 0.17426 0.17104 0.1805 0.23453 0.1999 RANDOM 15.696
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] 0.16 0.73 -0.58 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.808 r_dihedral_angle_3_deg 15.274 r_dihedral_angle_4_deg 14.959 r_dihedral_angle_1_deg 5.814 r_scangle_it 2.392 r_scbond_it 1.41 r_angle_refined_deg 1.332 r_mcangle_it 0.862 r_mcbond_it 0.439 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.808 r_dihedral_angle_3_deg 15.274 r_dihedral_angle_4_deg 14.959 r_dihedral_angle_1_deg 5.814 r_scangle_it 2.392 r_scbond_it 1.41 r_angle_refined_deg 1.332 r_mcangle_it 0.862 r_mcbond_it 0.439 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2276 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling