4XZM

Crystal structure of the methylated wild-type AKR1B10 holoenzyme


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 293.0
Details 30% PEG 6000, 100 mM sodium cacodylate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.43 α = 90
b = 79.43 β = 90
c = 49.8 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 2M -- 2011-03-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 0.92020 SLS X06DA

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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
1.75 50 99.0 -- 0.065 -- 3.2 -- 35411 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.75 1.81 100.0 0.375 -- 2.97 3.0 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.75 34.396 -- 1.42 -- 35411 1751 99.68 -- 0.2054 0.203 0.2499 Random 5%
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.747 1.794 -- 146 2615 0.2867 0.2879 -- 95.0
X Ray Diffraction 1.794 1.8464 -- 154 2633 0.2867 0.2712 -- 94.0
X Ray Diffraction 1.8464 1.9056 -- 102 2568 0.2805 0.3064 -- 96.0
X Ray Diffraction 1.9056 1.9732 -- 146 2550 0.2548 0.2615 -- 95.0
X Ray Diffraction 1.9732 2.0516 -- 148 2606 0.2564 0.2551 -- 95.0
X Ray Diffraction 2.0516 2.144 -- 130 2603 0.2493 0.2583 -- 95.0
X Ray Diffraction 2.144 2.2558 -- 116 2613 0.2354 0.2395 -- 96.0
X Ray Diffraction 2.2558 2.3953 -- 145 2569 0.2404 0.2571 -- 95.0
X Ray Diffraction 2.3953 2.5772 -- 130 2571 0.2436 0.2934 -- 95.0
X Ray Diffraction 2.5772 2.8311 -- 164 2610 0.2272 0.2641 -- 94.0
X Ray Diffraction 2.8311 3.2284 -- 116 2593 0.2039 0.2686 -- 96.0
X Ray Diffraction 3.2284 4.022 -- 113 2599 0.158 0.2332 -- 96.0
X Ray Diffraction 4.022 9.9295 -- 141 2571 0.1501 0.2241 -- 94.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_dihedral_angle_d 15.045
f_bond_d 0.008
f_angle_d 1.266
f_chiral_restr 0.077
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2571
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 178

Software

Software
Software Name Purpose
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.8_1069)

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