8FH7 | pdb_00008fh7

Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And AT-003

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	25%PEG 3,350, 100 mM Bis-Tris

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.186	α = 75.771
b = 46.957	β = 67.466
c = 47.379	γ = 76.871

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS 6M		2019-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

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	1.45	36.733	81.7	0.058	0.082	0.058	0.999	11.3	2		44438

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	1.45	1.47			0.418	0.591	0.418	0.687		2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.45	36.733	44436	2219	81.691	0.146	0.1451	0.1439	0.1689	0.1648	0.05	16.608

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]
-0.106	0.099	0.53	-0.158	-0.313	0.481

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.808
r_dihedral_angle_3_deg	13.662
r_dihedral_angle_2_deg	7.367
r_lrange_it	5.905
r_lrange_other	5.88
r_dihedral_angle_1_deg	5.843
r_scangle_it	5.029
r_scangle_other	5.028
r_scbond_it	3.27
r_scbond_other	3.269
r_mcangle_it	2.651
r_mcangle_other	2.65
r_angle_refined_deg	1.845
r_mcbond_it	1.771
r_mcbond_other	1.771
r_dihedral_angle_other_2_deg	1.033
r_angle_other_deg	0.584
r_symmetry_nbd_refined	0.295
r_nbd_refined	0.22
r_symmetry_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.188
r_nbd_other	0.188
r_symmetry_nbd_other	0.185
r_xyhbond_nbd_refined	0.111
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.082
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2518
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing