X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 289.0
Details 0.1M Tris-HCl, 0.25M NaCl and 20% polyethylene glycol 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.71 α = 90
b = 48.71 β = 90
c = 131.01 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 225 mm CCD Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror 2013-04-03
Diffraction Radiation
Monochromator Protocol
double crystal - liqued nitrogen cooled 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
1.85 70 97.7 0.076 -- -- 12.0 -- 13918 -- -3.0 26.42
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)
1.85 1.92 80.4 0.501 -- 1.8 3.9 1103

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 1.851 34.44 -- 1.34 -- 13843 689 97.63 -- 0.1889 0.1868 0.2339 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 1.851 1.9939 2296 136 2296 0.2345 0.2768 -- 89.0
X Ray Diffraction 1.9939 2.1946 2638 133 2638 0.1978 0.2477 -- 100.0
X Ray Diffraction 2.1946 2.512 2651 146 2651 0.194 0.2297 -- 100.0
X Ray Diffraction 2.512 3.1645 2697 143 2697 0.2094 0.3047 -- 100.0
X Ray Diffraction 3.1645 34.4456 2872 131 2872 0.1648 0.1873 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model FLAT BULK SOLVENT MODEL
Mean Isotropic B 21.9
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.063
f_dihedral_angle_d 26.221
f_angle_d 1.313
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 694
Nucleic Acid Atoms 406
Heterogen Atoms 13
Solvent Atoms 134

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.1_1168) refinement
PHENIX model building
HKL-2000 data collection