X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details Protein at 5mg/ml, 30% PEG 1500, 15mM ammonium sulfate, 20mM 2-mercaptoethanol, 3% w/v 1,5-Diaminopentane dihydrochloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 157.85 α = 90
b = 94.93 β = 122.75
c = 131.44 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 173
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2011-05-08
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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
3.1 19.9 99.6 -- -- -- 6.2 29851 29732 1.34 1.34 --
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)
3.1 3.2 98.6 -- -- 2.05 5.2 --

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 3.095 19.888 -- 1.34 29851 29732 1507 99.6 -- 0.2344 0.2317 0.2849 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 3.0954 3.1949 -- 115 2513 0.3319 0.3615 -- 97.0
X Ray Diffraction 3.1949 3.3086 -- 149 2540 0.2832 0.3704 -- 100.0
X Ray Diffraction 3.3086 3.4404 -- 126 2577 0.2625 0.3229 -- 100.0
X Ray Diffraction 3.4404 3.5961 -- 135 2554 0.2322 0.2866 -- 100.0
X Ray Diffraction 3.5961 3.7845 -- 138 2577 0.2208 0.2752 -- 100.0
X Ray Diffraction 3.7845 4.0197 -- 134 2570 0.2251 0.3057 -- 100.0
X Ray Diffraction 4.0197 4.3272 -- 135 2541 0.2013 0.2336 -- 100.0
X Ray Diffraction 4.3272 4.7572 -- 146 2580 0.1912 0.2284 -- 100.0
X Ray Diffraction 4.7572 5.4333 -- 157 2569 0.2128 0.3098 -- 100.0
X Ray Diffraction 5.4333 6.7996 -- 142 2582 0.2552 0.3007 -- 100.0
X Ray Diffraction 6.7996 19.8883 -- 130 2622 0.2349 0.2667 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -5.8616
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.2716
Anisotropic B[2][2] 6.6666
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.8914
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.056
f_dihedral_angle_d 14.306
f_angle_d 0.77
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9080
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 21

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
Phaser model building
MAR345dtb data collection