X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 298.0
Details PEG6K, LiCl, cacodylate, pH 5.8, vapor diffusion, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 94.43 α = 90
b = 94.43 β = 90
c = 188.18 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
IMAGE PLATE RIGAKU RAXIS IV++ -- 2000-09-04
Diffraction Radiation
Monochromator Protocol
HiRes2 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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
2.3 45.72 99.7 0.06 -- -- 3.87 -- 38507 -- -- --
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)
2.3 2.38 100.0 0.477 -- 2.3 3.89 3772

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
-- 2.3 45.717 -- 0.03 -- 37163 1924 96.21 -- 0.214 0.212 0.247 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 2.3 2.358 -- 133 2430 0.33 0.361 -- 95.0
X Ray Diffraction 2.358 2.421 -- 135 2436 0.314 0.356 -- 95.0
X Ray Diffraction 2.421 2.493 -- 132 2432 0.274 0.311 -- 95.0
X Ray Diffraction 2.493 2.573 -- 133 2488 0.254 0.262 -- 96.0
X Ray Diffraction 2.573 2.665 -- 137 2457 0.245 0.288 -- 96.0
X Ray Diffraction 2.665 2.772 -- 132 2478 0.249 0.336 -- 95.0
X Ray Diffraction 2.772 2.898 -- 137 2477 0.243 0.285 -- 97.0
X Ray Diffraction 2.898 3.05 -- 135 2496 0.249 0.28 -- 96.0
X Ray Diffraction 3.05 3.241 -- 137 2527 0.241 0.279 -- 97.0
X Ray Diffraction 3.241 3.492 -- 140 2525 0.223 0.302 -- 97.0
X Ray Diffraction 3.492 3.843 -- 136 2529 0.199 0.244 -- 96.0
X Ray Diffraction 3.843 4.399 -- 143 2587 0.17 0.203 -- 98.0
X Ray Diffraction 4.399 5.54 -- 145 2642 0.157 0.175 -- 98.0
X Ray Diffraction 5.54 45.726 -- 149 2735 0.188 0.21 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 60.298
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.889
f_angle_d 1.089
f_chiral_restr 0.068
f_bond_d 0.008
f_plane_restr 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4099
Nucleic Acid Atoms 0
Heterogen Atoms 74
Solvent Atoms 145

Software

Software
Software Name Purpose
d*TREK data processing version: 9.7 W8RSSI
PHENIX refinement
PDB_EXTRACT data extraction version: 3.005
CrystalClear data collection
d*TREK data reduction
d*TREK data scaling
PHENIX phasing