2RH8

Structure of apo anthocyanidin reductase from vitis vinifera


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5293NH4 acetate 150 mM, PEG 3350, Hepes 100 mM, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.244.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.47α = 90
b = 50.47β = 90
c = 440.406γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MIRRORS2007-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.2243.72796.40.0870.0875.611.71725342.07
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)
2.222.3498.80.3430.343212.2

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2C292.2230171141711485195.70.2030.1990.27RANDOM34.07
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]
0.880.440.88-1.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.824
r_dihedral_angle_4_deg19.97
r_dihedral_angle_3_deg14.543
r_scangle_it5.915
r_dihedral_angle_1_deg5.765
r_mcangle_it4.565
r_scbond_it4.303
r_mcbond_it3.21
r_angle_refined_deg2.068
r_angle_other_deg1.229
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.824
r_dihedral_angle_4_deg19.97
r_dihedral_angle_3_deg14.543
r_scangle_it5.915
r_dihedral_angle_1_deg5.765
r_mcangle_it4.565
r_scbond_it4.303
r_mcbond_it3.21
r_angle_refined_deg2.068
r_angle_other_deg1.229
r_mcbond_other0.695
r_symmetry_hbond_refined0.345
r_nbd_refined0.21
r_nbd_other0.184
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.177
r_symmetry_vdw_other0.175
r_chiral_restr0.118
r_symmetry_vdw_refined0.118
r_nbtor_other0.09
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2309
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms1

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction