2BRT

ANTHOCYANIDIN SYNTHASE FROM ARABIDOPSIS THALIANA COMPLEXED with naringenin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GP4PDB ENTRY 1GP4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.518% (W/V) PEG 2000 MONOMETHYLETHER, 50MM MES, 200MM AMMONIUM ACETATE, 2MM FESO4, 10MM POTASSIUM ALPHA-KETOGLUTARATE, 10MM SODIUM ASCORBATE, 2.5MM RACEMIC NARINGENIN IN 10% (V/V) MEOH, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.3347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.807α = 90
b = 62.309β = 90
c = 102.493γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRROR2001-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.2SRSPX14.2

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
12.240980.0815.85.91860742.5
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)
12.22.3199.50.613.15.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1GP42.253.2217793785970.2110.2080.268RANDOM43.42
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]
-0.542.31-1.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.807
r_dihedral_angle_3_deg16.659
r_dihedral_angle_4_deg15.978
r_dihedral_angle_1_deg7.457
r_scangle_it3.245
r_scbond_it2.24
r_angle_refined_deg1.887
r_mcangle_it1.316
r_angle_other_deg0.913
r_mcbond_it0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.807
r_dihedral_angle_3_deg16.659
r_dihedral_angle_4_deg15.978
r_dihedral_angle_1_deg7.457
r_scangle_it3.245
r_scbond_it2.24
r_angle_refined_deg1.887
r_mcangle_it1.316
r_angle_other_deg0.913
r_mcbond_it0.85
r_symmetry_vdw_refined0.314
r_nbd_refined0.216
r_xyhbond_nbd_refined0.194
r_nbd_other0.193
r_nbtor_refined0.185
r_symmetry_vdw_other0.183
r_symmetry_hbond_refined0.169
r_chiral_restr0.103
r_nbtor_other0.09
r_bond_refined_d0.025
r_gen_planes_refined0.007
r_bond_other_d0.002
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2685
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing