X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 298.0
Details 0.1 M sodium acetate pH 5.5, 0.2 M NaCl. 18% PEG-6000, 10 mM yttrium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.7 α = 90
b = 103.63 β = 90
c = 125.17 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-05-20
Diffraction Radiation
Monochromator Protocol
Double crystal, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.1 .979 ALS 8.2.1

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
2.35 39.9 99.7 -- -- -- 14.3 -- 22419 -- -3.0 --
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)
2.35 2.43 100.0 -- -- -- 14.6 --

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
SAD 2.353 39.9 -- 1.35 -- 22333 1145 99.72 -- 0.1828 0.1804 0.2287 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 2.3531 2.4602 -- 161 2582 0.216 0.2697 -- 100.0
X Ray Diffraction 2.4602 2.5899 -- 144 2600 0.2201 0.2836 -- 100.0
X Ray Diffraction 2.5899 2.7521 -- 146 2639 0.2163 0.2793 -- 100.0
X Ray Diffraction 2.7521 2.9645 -- 143 2614 0.2121 0.3096 -- 100.0
X Ray Diffraction 2.9645 3.2628 -- 135 2656 0.1989 0.2666 -- 100.0
X Ray Diffraction 3.2628 3.7346 -- 147 2650 0.1783 0.2114 -- 100.0
X Ray Diffraction 3.7346 4.704 -- 131 2701 0.1484 0.1777 -- 100.0
X Ray Diffraction 4.704 39.9179 -- 138 2746 0.1656 0.2054 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 12.8324
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.9227
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.9097
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.075
f_dihedral_angle_d 13.922
f_angle_d 1.079
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2916
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 77

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
AFRO/CRUNCH2 Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
AFRO/CRUNCH2 model building
HKL-2000 data collection