3I6I

Structure of the binary complex leucoanthocyanidin reductase - NADPH from vitis vinifera

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	Sodium acetate 0.36M, PEG 4000 38%, Tris 100mM, NaN3 3mM, glycerol 2.5%, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.079	α = 90
b = 50.236	β = 103.56
c = 67.424	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 225 mm CCD	Pt coated mirrors in a kirkpatrick-Baez (KB) geometry	2008-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8726	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	65.51	94.8	0.077	6.7	2.9	28119	28119			15.161

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.84	94.8		0.339	2	2.6	4067

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3I52	1.75	40.62	26688	26688	1414	94.44	0.15419	0.15204	0.19618	RANDOM	6.987

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]
0.51		0.45	-0.2		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.84
r_dihedral_angle_4_deg	13.578
r_dihedral_angle_3_deg	12.644
r_dihedral_angle_1_deg	5.777
r_scangle_it	5.434
r_scbond_it	3.881
r_mcangle_it	3.27
r_mcbond_it	2.195
r_angle_refined_deg	1.51
r_angle_other_deg	0.999

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.84
r_dihedral_angle_4_deg	13.578
r_dihedral_angle_3_deg	12.644
r_dihedral_angle_1_deg	5.777
r_scangle_it	5.434
r_scbond_it	3.881
r_mcangle_it	3.27
r_mcbond_it	2.195
r_angle_refined_deg	1.51
r_angle_other_deg	0.999
r_mcbond_other	0.568
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2303
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	52

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.