3I5M

Structure of the apo form of leucoanthocyanidin reductase from vitis vinifera


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3I52 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293PEG 4000 35%, sodium acetate 340mM, Tris 0.1M, sodium azide 3mM, glycerol 3.5%, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0138.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.421α = 90
b = 50.715β = 103.18
c = 68.051γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDPt coated mirrors in a Kirkpatrick-Baez (KB) geometry2008-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.7266.23900.10752.57546754644
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.722.8792.50.29422.51132

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 REPLACEMENTTHROUGHOUT3I522.7266.237060706035089.740.174260.174260.171040.23453RANDOM15.696
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]
0.160.73-0.580.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.808
r_dihedral_angle_3_deg15.274
r_dihedral_angle_4_deg14.959
r_dihedral_angle_1_deg5.814
r_scangle_it2.392
r_scbond_it1.41
r_angle_refined_deg1.332
r_mcangle_it0.862
r_mcbond_it0.439
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.808
r_dihedral_angle_3_deg15.274
r_dihedral_angle_4_deg14.959
r_dihedral_angle_1_deg5.814
r_scangle_it2.392
r_scbond_it1.41
r_angle_refined_deg1.332
r_mcangle_it0.862
r_mcbond_it0.439
r_chiral_restr0.09
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2276
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms

Software

Software
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling