2PZN

The crystallographic structure of Aldose Reductase IDD393 complex confirms Leu300 as a specificity determinant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T41ALDOSE REDUCTASE COMPLEXED WITH IDDD552 (PDB ID: 1T41)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5298Protein was co-crystallized with NADP+ (Sigma) and inhibitor (ratios protein/coenzyme/inhibitor = 1/2/2). Previously equilibrated (ammonium citrate buffer, PEG 6000 (15%)) hanging drops were seeded with stock seed solutions diluted 100 times. Cryofreezing was carried out through quick transfers into a stabilization solution (25% PEG 6000), then into a cryo-protecting solution (40% PEG 6000) and finally into either liquid nitrogen or ethane, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2144.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.224α = 67.58
b = 47.154β = 76.47
c = 40.316γ = 76.11
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-21.02-M FLAT MIRROR MADE OF ZERODUR PROVIDING VERTICAL FOCUSING AND REJECTION HARMONIC CONTAMINATION1999-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.90042APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
115094.910.06213.65167901158045
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.0485.60.2713.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE RALDOSE REDUCTASE COMPLEXED WITH IDDD552 (PDB ID: 1T41)11015804514998390.20.1286RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
1102439.162996.72
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.113
s_non_zero_chiral_vol0.101
s_zero_chiral_vol0.096
s_similar_adp_cmpnt0.049
s_anti_bump_dis_restr0.036
s_angle_d0.033
s_from_restr_planes0.0296
s_bond_d0.014
s_rigid_bond_adp_cmpnt0.005
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2936
Nucleic Acid Atoms
Solvent Atoms428
Heterogen Atoms73

Software

Software
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
Propietarydata collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing