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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
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 2.45 49.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.825 α = 90 b = 90.143 β = 90 c = 93.297 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 315 mirrors 2005-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.04 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 2.1 64.827 85.9 0.136 0.136 3.7 5.4 37210 37210 34.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.21 89.1 1.9 5.3 5566
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 2c29 2.1 64.82 37159 37159 1899 84.65 0.192 0.192 0.19 0.1823 0.242 0.2356 RANDOM 37.017
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] -0.33 2.47 -2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.562 r_dihedral_angle_4_deg 16.11 r_dihedral_angle_3_deg 14.509 r_dihedral_angle_1_deg 5.187 r_scangle_it 2.537 r_mcangle_it 2.534 r_scbond_it 1.683 r_mcbond_it 1.519 r_angle_refined_deg 1.271 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.562 r_dihedral_angle_4_deg 16.11 r_dihedral_angle_3_deg 14.509 r_dihedral_angle_1_deg 5.187 r_scangle_it 2.537 r_mcangle_it 2.534 r_scbond_it 1.683 r_mcbond_it 1.519 r_angle_refined_deg 1.271 r_nbtor_refined 0.304 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.15 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5027 Nucleic Acid Atoms Solvent Atoms 558 Heterogen Atoms 138
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction AMoRE phasing