X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 28% w/v PEG2000 MME, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 35.46 α = 90
b = 37.33 β = 90
c = 69.29 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
2 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2011-04-19
CCD NOIR-1 -- 2011-04-22
Diffraction Radiation
Monochromator Protocol
osmic mirrors SINGLE WAVELENGTH
sagitally focused Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.54178 -- --
SYNCHROTRON ALS BEAMLINE 4.2.2 1.37757 ALS 4.2.2

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
1.45 50 99.9 0.035 -- -- 11.4 16959 16813 0.0 0.0 --
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)
1.45 1.48 100.0 0.363 -- 6.3 10.6 --

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 1.5 20.645 -- 1.34 15410 15310 1567 99.96 -- 0.2166 0.2134 0.243 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 1.5 1.5484 -- 124 1245 0.232 0.2561 -- 100.0
X Ray Diffraction 1.5484 1.6037 -- 146 1215 0.2082 0.2672 -- 100.0
X Ray Diffraction 1.6037 1.6679 -- 139 1219 0.1979 0.2503 -- 100.0
X Ray Diffraction 1.6679 1.7438 -- 141 1226 0.2099 0.23 -- 100.0
X Ray Diffraction 1.7438 1.8357 -- 144 1242 0.2192 0.2425 -- 100.0
X Ray Diffraction 1.8357 1.9506 -- 154 1212 0.2195 0.2467 -- 100.0
X Ray Diffraction 1.9506 2.1011 -- 155 1237 0.2234 0.2701 -- 100.0
X Ray Diffraction 2.1011 2.3123 -- 132 1255 0.22 0.2631 -- 100.0
X Ray Diffraction 2.3123 2.6463 -- 135 1256 0.2243 0.2354 -- 100.0
X Ray Diffraction 2.6463 3.3317 -- 143 1283 0.2236 0.271 -- 100.0
X Ray Diffraction 3.3317 20.6471 -- 154 1353 0.1971 0.2125 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 3.0013
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.5114
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.49
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.045
f_dihedral_angle_d 13.56
f_angle_d 0.766
f_bond_d 0.02
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 783
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 123

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: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
PHENIX model building
HKL-2000 data collection