X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details PDE9A2 (15 mg/mL) in a buffer of 50 mM NaCl, 20 mM Tris.HCl pH 7.5, 1 mM beta-mercaptoethanol and 1 mM EDTA was mixed with 2 mM IBMX for 2h before setting-up of crystallization against the well buffer of 2.0 M Na formate, 0.1 M HEPES pH 7.5, 5% xylitol at 4C. The PDE9A-IBMX complex crystals were formed after 1d and reached the maximum size in 2 weeks. Crystals of the PDE9A-28 complex were prepared by soaking PDE9-IBMX co-crystals in the crystallization buffer plus 5 mM 28 at 25C for 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.28 α = 90
b = 104.28 β = 90
c = 270.07 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0 PHOTON FACTORY BL-17A

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
2.7 30 99.7 0.093 -- -- -- -- 41120 0.0 0.0 --

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 2.7 30.0 0.0 0.0 -- 38971 3897 -- -- -- 0.212 0.245 Random
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 52.8
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.007
c_angle_deg 1.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5390
Nucleic Acid Atoms 0
Heterogen Atoms 97
Solvent Atoms 18

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
AMoRE Structure Solution
CNS1.2 Structure Refinement
Software
Software Name Purpose
CNS1.2 refinement
AMoRE model building