2NNL

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 2C29 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.929850MM NACL, 29% PEG3350, 100MM HEPES, 3MM NAN3, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4549.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.825α = 90
b = 90.143β = 90
c = 93.297γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2005-11-05MSINGLE 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
12.164.82785.90.1360.1363.75.4372103721034.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.2189.11.95.35566

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 REPLACEMENTTHROUGHOUT2c292.164.823715937159189984.650.1920.1920.190.242RANDOM37.017
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]
-0.332.47-2.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.562
r_dihedral_angle_4_deg16.11
r_dihedral_angle_3_deg14.509
r_dihedral_angle_1_deg5.187
r_scangle_it2.537
r_mcangle_it2.534
r_scbond_it1.683
r_mcbond_it1.519
r_angle_refined_deg1.271
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.562
r_dihedral_angle_4_deg16.11
r_dihedral_angle_3_deg14.509
r_dihedral_angle_1_deg5.187
r_scangle_it2.537
r_mcangle_it2.534
r_scbond_it1.683
r_mcbond_it1.519
r_angle_refined_deg1.271
r_nbtor_refined0.304
r_nbd_refined0.191
r_symmetry_vdw_refined0.189
r_xyhbond_nbd_refined0.166
r_symmetry_hbond_refined0.15
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5027
Nucleic Acid Atoms
Solvent Atoms558
Heterogen Atoms138

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
AMoREphasing