8FH8 | pdb_00008fh8

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

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
2.24	45.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.061	α = 77.105
b = 46.989	β = 66.937
c = 48.237	γ = 77.235

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		2019-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.96584	SSRL	BL9-2

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	1.6	36.475	90.5	0.035	0.05	0.035	0.999	17.4	3.8		37282

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	1.6	1.63			0.216	0.306	0.216	0.962		3.8

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	1.6	36.475	37281	1845	90.536	0.168	0.1666	0.18	0.1948	0.2	0.05	18.543

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]
-1.248	0.524	0.916	-0.164	-1.527	1.561

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.279
r_dihedral_angle_3_deg	13.491
r_dihedral_angle_2_deg	6.393
r_dihedral_angle_1_deg	6.007
r_lrange_it	5.44
r_lrange_other	5.439
r_scangle_it	4.604
r_scangle_other	4.604
r_scbond_it	3.07
r_scbond_other	3.069
r_mcangle_it	2.649
r_mcangle_other	2.648
r_mcbond_it	1.849
r_mcbond_other	1.84
r_angle_refined_deg	1.714
r_dihedral_angle_other_2_deg	0.661
r_angle_other_deg	0.565
r_nbd_refined	0.215
r_symmetry_nbd_refined	0.195
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.185
r_nbd_other	0.182
r_xyhbond_nbd_refined	0.128
r_symmetry_xyhbond_nbd_refined	0.101
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.079
r_gen_planes_refined	0.011
r_bond_refined_d	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	2517
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	116

Software

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