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Structure of the binary complex leucoanthocyanidin reductase - NADPH 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 Sodium acetate 0.36M, PEG 4000 38%, Tris 100mM, NaN3 3mM, glycerol 2.5%, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.95 36.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.079 α = 90 b = 50.236 β = 103.56 c = 67.424 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 2008-11-08 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 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 1.75 65.51 94.8 0.077 6.7 2.9 28119 28119 15.161
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.84 94.8 0.339 2 2.6 4067
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 (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 1.75 40.62 26688 26688 1414 94.44 0.15419 0.15204 0.1641 0.19618 0.2068 RANDOM 6.987
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] 0.51 0.45 -0.2 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.84 r_dihedral_angle_4_deg 13.578 r_dihedral_angle_3_deg 12.644 r_dihedral_angle_1_deg 5.777 r_scangle_it 5.434 r_scbond_it 3.881 r_mcangle_it 3.27 r_mcbond_it 2.195 r_angle_refined_deg 1.51 r_angle_other_deg 0.999
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.84 r_dihedral_angle_4_deg 13.578 r_dihedral_angle_3_deg 12.644 r_dihedral_angle_1_deg 5.777 r_scangle_it 5.434 r_scbond_it 3.881 r_mcangle_it 3.27 r_mcbond_it 2.195 r_angle_refined_deg 1.51 r_angle_other_deg 0.999 r_mcbond_other 0.568 r_chiral_restr 0.108 r_bond_refined_d 0.016 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 2303 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 52
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling