X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 283.0
Details Protein solution (10 mg/mL dGTPase, 20mM Tris-HCl, pH 7.0, 1mM deoxy-CCC) mixed 1:1 with well solution (0.5mM NH4SO4, 0.1M NaCitrate, 1M LiSO4, pH 5.6). Cryo conditions are well solution mixed with 25% ethylene glycol.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 189.8 α = 90
b = 189.8 β = 90
c = 296.8 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2011-03-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM

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
3.35 20 98.6 0.147 -- -- 6.2 -- 76628 -- -- --
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)
3.35 3.47 98.7 0.699 -- 2.0 5.0 --

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 3.354 19.99 -- 0.0 -- 66200 3404 85.18 -- 0.1739 0.172 0.2088 --
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 3.3535 3.4728 -- 296 5547 0.2667 0.3015 -- 76.0
X Ray Diffraction 3.4728 3.611 -- 323 5678 0.2326 0.2761 -- 79.0
X Ray Diffraction 3.611 3.7744 -- 331 5822 0.205 0.2509 -- 80.0
X Ray Diffraction 3.7744 3.9719 -- 287 5907 0.1905 0.2285 -- 80.0
X Ray Diffraction 3.9719 4.2185 -- 321 6038 0.1701 0.2215 -- 82.0
X Ray Diffraction 4.2185 4.5407 -- 302 6211 0.1456 0.1906 -- 84.0
X Ray Diffraction 4.5407 4.9912 -- 360 6460 0.1361 0.1783 -- 88.0
X Ray Diffraction 4.9912 5.6988 -- 366 6682 0.1538 0.1998 -- 90.0
X Ray Diffraction 5.6988 7.1254 -- 404 7015 0.1763 0.21 -- 94.0
X Ray Diffraction 7.1254 19.99 -- 414 7436 0.162 0.1801 -- 96.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_dihedral_angle_d 15.717
f_chiral_restr 0.044
f_bond_d 0.014
f_angle_d 1.242
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 24119
Nucleic Acid Atoms 0
Heterogen Atoms 401
Solvent Atoms 18

Software

Software
Software Name Purpose
PHENIX refinement version: (phenix.refine: 1.9_1692)
HKL-2000 data reduction
HKL-2000 data scaling
MOLREP phasing