4QBX | pdb_00004qbx

Human Aldose Reductase complexed with a ligand with an IDD structure ({5-fluoro-2-[(3-nitrobenzyl)carbamoyl]phenoxy}acetic acid) at 0.98 A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DUX	pdb entry 2dux

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	291	Crystallization solution: 50 mM di-Ammoniumhydrogen citrate, PEG6000= 5 % (m/V) DTT= 5.15 g/L NADP+= 0.66 g/L and Human Aldose Reductase= 15 mg/ml. Afterwards the crystals were soaked into 120 mM di-Ammoniumhydrogen citrate pH 5.0 25% (m/V) PEG6000 saturated with the inhibitor. The well solution was 120mM di-Ammonium hydrogen citrate with 20% PEG6000 pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.383	α = 90
b = 66.856	β = 92.27
c = 47.405	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	Silicon, active surface 50 nm Rh-coated	2013-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91841	BESSY	14.2

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	0.98	50	100	0.06	22.1	3.7		175882			6.594

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	0.98	1	99.9		0.414	2.63	3.5	8807

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	pdb entry 2dux	0.98	17.434	1.36	175837	8801	99.94	0.1358	0.135	0.14	0.1514	0.15	random

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
f_dihedral_angle_d	16.251
f_angle_d	1.313
f_chiral_restr	0.081
f_plane_restr	0.007
f_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2460
Nucleic Acid Atoms
Solvent Atoms	396
Heterogen Atoms	86

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	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 R01GM157729.