7BC1 | pdb_00007bc1

Crystal structure of aldo-keto reductase from Agrobacterium tumefaciens in a ternary complex with NADPH and glucose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7BBY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	0.1 M SPG 25% PEG 1500 In-drop protein concentration of 13 mg/ml

Crystal Properties
Matthews coefficient	Solvent content
2.2328458	44.947571

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.853	α = 90
b = 82.853	β = 90
c = 77.255	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2019-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.5	52.57	100	0.082	0.086	0.025	0.999	14.7	11.9		48238

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	99.9		1.67	1.77	0.582	0.746		9

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7BBY	1.5	52.51	45844	2368	99.96	0.1672	0.1658	0.18	0.1945	0.21	RANDOM	21.006

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]
-1.19	-0.59		-1.19		3.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.731
r_dihedral_angle_4_deg	17.249
r_dihedral_angle_3_deg	11.707
r_dihedral_angle_1_deg	6.082
r_angle_refined_deg	1.725
r_angle_other_deg	1.532
r_chiral_restr	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.731
r_dihedral_angle_4_deg	17.249
r_dihedral_angle_3_deg	11.707
r_dihedral_angle_1_deg	6.082
r_angle_refined_deg	1.725
r_angle_other_deg	1.532
r_chiral_restr	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2178
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
REFMAC	phasing

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 R01GM157729.