X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 292.0
Details 6% PEG20,000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.19 α = 90
b = 213.51 β = 99.64
c = 86.27 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2009-11-04
Diffraction Radiation
Monochromator Protocol
Si mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 1.2827 APS 24-ID-C

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 30 99.3 -- -- -- -- 58980 58596 -- -1.0 --
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)
3.0 3.11 99.0 -- 0.512 1.9 2.9 5839

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
-- 3.0 29.819 -- 0.0 58596 57011 1930 96.55 -- 0.213 0.2111 0.2659 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 3.0 3.1092 -- 174 5074 0.3228 0.3539 -- 89.0
X Ray Diffraction 3.1092 3.2336 -- 187 5250 0.2923 0.3675 -- 93.0
X Ray Diffraction 3.2336 3.3805 -- 182 5395 0.2614 0.3178 -- 95.0
X Ray Diffraction 3.3805 3.5585 -- 197 5490 0.24 0.3076 -- 96.0
X Ray Diffraction 3.5585 3.781 -- 196 5573 0.2217 0.3037 -- 98.0
X Ray Diffraction 3.781 4.0723 -- 192 5566 0.2018 0.2569 -- 98.0
X Ray Diffraction 4.0723 4.4809 -- 198 5645 0.1775 0.2472 -- 99.0
X Ray Diffraction 4.4809 5.1264 -- 202 5686 0.1696 0.2052 -- 99.0
X Ray Diffraction 5.1264 6.448 -- 199 5696 0.2093 0.2477 -- 99.0
X Ray Diffraction 6.448 29.8207 -- 203 5706 0.1868 0.2434 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 9.845
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 8.5073
Anisotropic B[2][2] -13.866
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.021
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.06
f_dihedral_angle_d 18.667
f_angle_d 0.97
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13963
Nucleic Acid Atoms 1546
Heterogen Atoms 60
Solvent Atoms 24

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SHARP Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
SHARP model building
MAR345dtb data collection