X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details 20% (w/v) PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, 5 mM spermine-HCl, 50 mM HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 225.13 α = 90
b = 69.21 β = 106.43
c = 104.14 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 Monochromator 2012-08-03
Diffraction Radiation
Monochromator Protocol
Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A

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
2.85 36.64 98.43 0.099 0.097 -- 3.8 35694 35694 1.5 1.5 83.42
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)
2.85 2.9 98.6 0.411 0.546 2.7 3.7 1780

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 2.85 36.639 1.35 1.35 35785 35694 1999 98.43 0.2357 0.2334 0.2334 0.2733 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 2.85 2.9212 2369 140 2369 0.3191 0.3642 -- 98.0
X Ray Diffraction 2.9212 3.0002 2398 143 2398 0.3183 0.353 -- 99.0
X Ray Diffraction 3.0002 3.0884 2383 141 2383 0.3004 0.3251 -- 99.0
X Ray Diffraction 3.0884 3.1881 2402 143 2402 0.276 0.3398 -- 99.0
X Ray Diffraction 3.1881 3.3019 2393 143 2393 0.2772 0.3335 -- 99.0
X Ray Diffraction 3.3019 3.434 2412 142 2412 0.2673 0.3298 -- 99.0
X Ray Diffraction 3.434 3.5902 2408 144 2408 0.2778 0.3223 -- 99.0
X Ray Diffraction 3.5902 3.7793 2423 143 2423 0.2593 0.3249 -- 99.0
X Ray Diffraction 3.7793 4.0158 2420 144 2420 0.2422 0.3094 -- 99.0
X Ray Diffraction 4.0158 4.3254 2444 145 2444 0.2146 0.2334 -- 99.0
X Ray Diffraction 4.3254 4.7599 2415 142 2415 0.1983 0.2356 -- 99.0
X Ray Diffraction 4.7599 5.4467 2445 146 2445 0.2014 0.26 -- 100.0
X Ray Diffraction 5.4467 6.855 2470 146 2470 0.2374 0.2693 -- 100.0
X Ray Diffraction 6.855 36.6419 2313 137 2313 0.2064 0.2227 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 60.2555
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.063
f_plane_restr 0.004
f_chiral_restr 0.068
f_angle_d 0.912
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7996
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 45

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
HKL data reduction