X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 0.7M sodium citrate, 10mM DTT, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.69 α = 90
b = 89.9 β = 90
c = 99.79 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 RIGAKU SATURN 944 -- 2009-11-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5419 -- --

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 40.98 99.0 -- -- -- -- -- 48448 2.0 2.0 --
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)
2.0 2.07 99.9 -- -- -- -- --

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 2.0 40.983 -- -- 48448 46290 2348 95.43 -- 0.1886 0.1875 0.2078 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 2.0 2.0408 -- 108 2421 0.2381 0.3232 -- 90.0
X Ray Diffraction 2.0408 2.0852 -- 144 2452 0.2266 0.2349 -- 92.0
X Ray Diffraction 2.0852 2.1337 -- 122 2482 0.2074 0.2992 -- 92.0
X Ray Diffraction 2.1337 2.1871 -- 136 2454 0.2065 0.2524 -- 92.0
X Ray Diffraction 2.1871 2.2462 -- 131 2481 0.1975 0.2491 -- 93.0
X Ray Diffraction 2.2462 2.3123 -- 123 2504 0.1897 0.2091 -- 93.0
X Ray Diffraction 2.3123 2.3869 -- 123 2529 0.1972 0.2257 -- 94.0
X Ray Diffraction 2.3869 2.4722 -- 122 2518 0.2018 0.2409 -- 94.0
X Ray Diffraction 2.4722 2.5712 -- 146 2539 0.2114 0.2341 -- 95.0
X Ray Diffraction 2.5712 2.6882 -- 124 2616 0.2183 0.2339 -- 96.0
X Ray Diffraction 2.6882 2.8299 -- 149 2604 0.1974 0.2262 -- 97.0
X Ray Diffraction 2.8299 3.0071 -- 143 2630 0.2032 0.2307 -- 98.0
X Ray Diffraction 3.0071 3.2392 -- 156 2671 0.1944 0.2354 -- 99.0
X Ray Diffraction 3.2392 3.565 -- 140 2719 0.1894 0.2029 -- 99.0
X Ray Diffraction 3.565 4.0805 -- 153 2721 0.1612 0.1661 -- 100.0
X Ray Diffraction 4.0805 5.1394 -- 162 2739 0.1516 0.1681 -- 99.0
X Ray Diffraction 5.1394 40.992 -- 166 2862 0.1862 0.1918 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.6675
Anisotropic B[1][1] -1.3823
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.8204
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.2027
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.319
f_plane_restr 0.005
f_chiral_restr 0.065
f_angle_d 0.966
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3438
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 330

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
d*TREK Data Reduction (intensity integration)
d*TREK Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
CrystalClear data collection