3C1T

Binding of two substrate analogue molecules to dihydroflavonol 4-reductase alters the functional geometry of the catalytic site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C29pdb entry 2c29

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.9293NaCl 50 mM, PEG 3350 29%, Hepes 100 mM, NaN3 3 mM, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.550.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.231α = 90
b = 177.958β = 104.77
c = 92.597γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2005-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.04ESRFID29

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.25289.0899.80.0790.0795.43.3694376943730
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)RedundancyNumber Unique Reflections (All)
2.2522.371000.2890.28923.310024

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 2c292.25289.096591065910348599.710.189430.189430.185910.25548RANDOM35.303
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]
0.15-0.681.71-2.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.877
r_dihedral_angle_3_deg15.464
r_dihedral_angle_4_deg15.034
r_dihedral_angle_1_deg5.81
r_angle_other_deg4.316
r_mcangle_it3.877
r_scangle_it3.828
r_scbond_it2.778
r_mcbond_it2.568
r_angle_refined_deg1.925
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.877
r_dihedral_angle_3_deg15.464
r_dihedral_angle_4_deg15.034
r_dihedral_angle_1_deg5.81
r_angle_other_deg4.316
r_mcangle_it3.877
r_scangle_it3.828
r_scbond_it2.778
r_mcbond_it2.568
r_angle_refined_deg1.925
r_symmetry_hbond_refined0.263
r_nbd_other0.235
r_symmetry_vdw_refined0.219
r_nbd_refined0.211
r_xyhbond_nbd_refined0.188
r_nbtor_refined0.187
r_symmetry_vdw_other0.178
r_nbtor_other0.113
r_chiral_restr0.104
r_bond_refined_d0.014
r_xyhbond_nbd_other0.008
r_gen_planes_other0.007
r_gen_planes_refined0.005
r_bond_other_d
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9981
Nucleic Acid Atoms
Solvent Atoms768
Heterogen Atoms376

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling