X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.6
Temperature 301.0
Details 50 mM imidazole pH 6.6, 100 mM ammonium sulfate, 15 mM manganese sulfate, 10 mM spermine, 5 mM TCEP, 11% (w/w) PEG 8000, and 5% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 301K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 162.65 α = 90
b = 72.99 β = 100.59
c = 109.6 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 0
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 -- 2010-07-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F1 -- CHESS F1

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
2.3 107.73 -- -- -- -- -- -- 55926 -- -- --

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 2.2964 41.294 -- 1.34 -- 55926 2000 98.81 -- 0.2175 0.2159 0.2603 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 2.2964 2.3538 -- 131 3557 0.2799 0.3493 -- 91.0
X Ray Diffraction 2.3538 2.4174 -- 138 3715 0.2708 0.3365 -- 97.0
X Ray Diffraction 2.4174 2.4885 -- 142 3804 0.2564 0.2734 -- 98.0
X Ray Diffraction 2.4885 2.5688 -- 142 3849 0.2354 0.3056 -- 99.0
X Ray Diffraction 2.5688 2.6606 -- 142 3822 0.2381 0.2844 -- 99.0
X Ray Diffraction 2.6606 2.7671 -- 144 3876 0.2326 0.2803 -- 99.0
X Ray Diffraction 2.7671 2.8931 -- 144 3869 0.2233 0.2824 -- 100.0
X Ray Diffraction 2.8931 3.0455 -- 144 3894 0.2329 0.3007 -- 100.0
X Ray Diffraction 3.0455 3.2363 -- 144 3863 0.2284 0.2793 -- 100.0
X Ray Diffraction 3.2363 3.486 -- 144 3911 0.2219 0.2568 -- 100.0
X Ray Diffraction 3.486 3.8366 -- 145 3908 0.2041 0.2486 -- 100.0
X Ray Diffraction 3.8366 4.3913 -- 145 3919 0.1724 0.2162 -- 100.0
X Ray Diffraction 4.3913 5.5304 -- 146 3928 0.1753 0.2207 -- 100.0
X Ray Diffraction 5.5304 41.3004 -- 149 4011 0.2391 0.2604 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -2.3086
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -2.6254
Anisotropic B[2][2] 1.3432
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.9654
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.06
f_dihedral_angle_d 15.773
f_angle_d 0.858
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7918
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 300

Software

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