X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
Temperature 277.0
Details Purified PDE2(215-900) was exchanged into crystallization buffer (50 mM HEPES pH7.5, 50 mM NaCl, and 2 mM TCEP) to a final concentration of 10mg/ml. Protein was mixed 1:1 with precipitant solution composed of 5-10% isopropanol, 0.1 M MES pH5.4-6.0, 0.2M Ca(OAc)2. Clusters of thin plate-like crystals appeared in 3-4 days, VAPOR DIFFUSION, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.23 α = 90
b = 89.7 β = 90
c = 264.19 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2006-10-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 1.28 ESRF ID14-4

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
3 50 99.8 0.141 -- -- 14.2 31872 31809 -- -3.0 93.975
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)
3.0 3.11 100.0 -- -- -- -- --

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 3.02 18.26 -- 0.0 -- 31511 1598 99.51 -- 0.2147 0.2096 0.311 RANDOM
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 3.02 3.2 -- 259 4679 0.2285 0.3983 -- 99.51
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 77.62
Anisotropic B[1][1] -17.2654
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -10.1738
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 27.4392
RMS Deviations
Key Refinement Restraint Deviation
t_trig_c_planes 0.012
t_angle_deg 1.381
t_it 2.303
t_bond_d 0.011
t_gen_planes 0.015
t_dihedral_angle_d 30.704
t_nbd 0.064
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10455
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 191

Software

Software
Software Name Purpose
HKL-2000 data collection
PHASER phasing
BUSTER-TNT refinement version: 2.1.1
HKL-2000 data reduction
HKL-2000 data scaling