7BBY | pdb_00007bby

Crystal structure of aldo-keto reductase with C-terminal His tag from Agrobacterium tumefaciens

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4R9O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.056 M sodium phosphate monobasic/monohydrate 1.344 M potassium phosphate dibasic protein at 20mg/ml

Crystal Properties
Matthews coefficient	Solvent content
3.26	62.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.928	α = 90
b = 108.928	β = 90
c = 108.928	γ = 90

Symmetry
Space Group	P 21 3

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		2018-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

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	1.83	44.51	100	0.189	0.193	0.039	0.999	14.1	24.5		38236

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	1.83	1.87	100		4.196	4.282	0.854	0.439		24.9

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	4r9o	1.83	44.47	36384	1822	99.98	0.1917	0.1909	0.2	0.2086	0.22	RANDOM	31.964

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.419
r_dihedral_angle_4_deg	17.68
r_dihedral_angle_3_deg	13.816
r_dihedral_angle_1_deg	5.867
r_angle_refined_deg	1.683
r_angle_other_deg	1.492
r_chiral_restr	0.082
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	31.419
r_dihedral_angle_4_deg	17.68
r_dihedral_angle_3_deg	13.816
r_dihedral_angle_1_deg	5.867
r_angle_refined_deg	1.683
r_angle_other_deg	1.492
r_chiral_restr	0.082
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	2234
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	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.