X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 296.0
Details 4% isopropanol, 50 mM sodium citrate, 600 nL + 400 nL (protein + precipitant) drop ratio, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 160.6 α = 90
b = 160.6 β = 90
c = 280.56 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD DECTRIS PILATUS 2M -- 2012-07-23
Diffraction Radiation
Monochromator Protocol
Single bounce monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92000 DIAMOND I04-1

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
3.7 72.19 99.75 0.124 0.124 -- 12.11 39884 39884 -1.0 -1.0 --
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)
3.7 3.9 100.0 0.45 -- 1.71 11.46 --

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 3.7 71.823 -- 1.34 39884 39825 2006 99.69 -- 0.1886 0.1855 0.2485 --
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 3.7 3.7925 -- 149 2649 0.1818 0.242 -- 100.0
X Ray Diffraction 3.7925 3.8951 -- 139 2672 0.1791 0.2446 -- 100.0
X Ray Diffraction 3.8951 4.0097 -- 154 2636 0.168 0.238 -- 100.0
X Ray Diffraction 4.0097 4.1391 -- 129 2683 0.1635 0.2386 -- 100.0
X Ray Diffraction 4.1391 4.287 -- 135 2655 0.1559 0.2329 -- 100.0
X Ray Diffraction 4.287 4.4586 -- 153 2681 0.1468 0.2442 -- 100.0
X Ray Diffraction 4.4586 4.6615 -- 127 2670 0.1398 0.1923 -- 100.0
X Ray Diffraction 4.6615 4.9072 -- 149 2689 0.1468 0.2478 -- 100.0
X Ray Diffraction 4.9072 5.2146 -- 138 2642 0.164 0.2114 -- 98.0
X Ray Diffraction 5.2146 5.6171 -- 154 2688 0.1773 0.269 -- 100.0
X Ray Diffraction 5.6171 6.1821 -- 134 2730 0.1972 0.2628 -- 100.0
X Ray Diffraction 6.1821 7.0759 -- 147 2738 0.1957 0.2841 -- 100.0
X Ray Diffraction 7.0759 8.9123 -- 147 2792 0.1823 0.2452 -- 100.0
X Ray Diffraction 8.9123 71.8361 -- 151 2894 0.255 0.2729 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 7.8718
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 7.8718
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -12.19
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.087
f_dihedral_angle_d 18.903
f_angle_d 1.396
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14849
Nucleic Acid Atoms 1374
Heterogen Atoms 3
Solvent Atoms 2

Software

Computing
Computing Package Purpose
GDE Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.2_869) refinement
Phaser model building
GDE data collection