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Binding of two substrate analogue molecules to dihydroflavonol-4-reductase alters the functional geometry of the catalytic site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C29 pdb entry 2c29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 298 50mM NaCl, 29% PEG3350, 100mM Hepes, 3mM NaN3, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.49 50.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.231 α = 90 b = 177.958 β = 104.77 c = 92.597 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 ADSC QUANTUM 210 MIRRORS 2005-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0400 ESRF ID29
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 2.06 89.535 99 0.093 0.093 4 3.2 89953 30
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) 2.06 2.17 94.1 0.505 0.505 2.1 2.5 12398
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 (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 pdb entry 2c29 2.06 89.44 89894 4501 98.88 0.193 0.193 0.189 0.1953 0.257 0.2608 RANDOM 35.307
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] 0.17 -0.85 2.1 -2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.877 r_dihedral_angle_3_deg 15.464 r_dihedral_angle_4_deg 15.034 r_dihedral_angle_1_deg 5.81 r_angle_other_deg 4.316 r_mcangle_it 3.877 r_scangle_it 3.828 r_scbond_it 2.778 r_mcbond_it 2.568 r_angle_refined_deg 1.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.877 r_dihedral_angle_3_deg 15.464 r_dihedral_angle_4_deg 15.034 r_dihedral_angle_1_deg 5.81 r_angle_other_deg 4.316 r_mcangle_it 3.877 r_scangle_it 3.828 r_scbond_it 2.778 r_mcbond_it 2.568 r_angle_refined_deg 1.925 r_symmetry_hbond_refined 0.263 r_nbd_other 0.235 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.187 r_symmetry_vdw_other 0.175 r_nbtor_other 0.113 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_xyhbond_nbd_other 0.008 r_gen_planes_other 0.007 r_gen_planes_refined 0.005 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9981 Nucleic Acid Atoms Solvent Atoms 768 Heterogen Atoms 376
Software Software Software Name Purpose SCALA data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction ProDC data collection MOSFLM data reduction