1GP6 | pdb_00001gp6

Anthocyanidin synthase from Arabidopsis thaliana complexed with trans-dihydroquercetin (with 30 min exposure to O2)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GP4	PDB ENTRY 1GP4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		18% (W/V) PEG 2000 MONOMETHYLETHER, 50 MM MES, 200 MM AMMONIUM ACETATE, 2 MM IRON(II) SULPHATE, 10 MM POTASSIUM ALPHA-KETOGLUTARATE, 10 MM SODIUM ASCORBATE 10 MM DHQ (IN MEOH TO GIVE A FINAL CONC. OF 10%(V/V) MEOH), PH 6.5, ANAEROBIC (AR ATMOSPHERE, < 0.5 PPM OXYGEN)

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.258	α = 90
b = 72.385	β = 90
c = 87.054	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC CCD	MIRRORS	2001-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6		SRS	PX9.6

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.75	25	99.9	0.068	14.9	3.8		39711			20

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.8	99.9		0.274	4.1	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1GP4	1.75	25	39703	1626	99.8	0.194	0.194	0.222	RANDOM	23.3

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]
-2.92			8.81		-5.89

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.8
c_scangle_it	3.04
c_scbond_it	2.1
c_mcangle_it	1.9
c_angle_deg	1.6
c_mcbond_it	1.25
c_improper_angle_d	1.07
c_bond_d	0.013
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2752
Nucleic Acid Atoms
Solvent Atoms	357
Heterogen Atoms	77

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing