X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microdialysis
pH 5.7
Temperature 298.0
Details 40 mM sodium citrate, 1 mM 2-mercaptoethanol, 0.2 mM EDTA, 1.0 mM CTP, pH 5.7, MICRODIALYSIS, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 121.3 α = 90
b = 121.3 β = 90
c = 142.25 γ = 120
Symmetry
Space Group P 3 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2012-01-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.542 -- --

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
2.1 43.22 100.0 0.057 -- -- 5.35 70735 70735 -- -3.0 --
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)
2.1 2.18 100.0 0.45 -- 2.6 5.28 6982

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 2.1 43.218 -- 0.0 70735 70722 3569 99.64 -- 0.186 0.1838 0.2291 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 2.1 2.1288 -- 131 2666 0.2637 0.3248 -- 100.0
X Ray Diffraction 2.1288 2.1592 -- 143 2634 0.2499 0.262 -- 100.0
X Ray Diffraction 2.1592 2.1914 -- 143 2658 0.2516 0.3272 -- 100.0
X Ray Diffraction 2.1914 2.2257 -- 155 2663 0.2416 0.3057 -- 100.0
X Ray Diffraction 2.2257 2.2621 -- 149 2668 0.2559 0.3465 -- 100.0
X Ray Diffraction 2.2621 2.3011 -- 120 2686 0.2589 0.3464 -- 100.0
X Ray Diffraction 2.3011 2.343 -- 160 2653 0.2513 0.3151 -- 100.0
X Ray Diffraction 2.343 2.3881 -- 146 2657 0.2369 0.3303 -- 100.0
X Ray Diffraction 2.3881 2.4368 -- 129 2686 0.2367 0.2591 -- 100.0
X Ray Diffraction 2.4368 2.4898 -- 143 2687 0.2392 0.2695 -- 100.0
X Ray Diffraction 2.4898 2.5477 -- 142 2660 0.2231 0.331 -- 100.0
X Ray Diffraction 2.5477 2.6114 -- 149 2640 0.2076 0.264 -- 100.0
X Ray Diffraction 2.6114 2.682 -- 156 2681 0.2157 0.3239 -- 100.0
X Ray Diffraction 2.682 2.7609 -- 145 2675 0.2154 0.266 -- 100.0
X Ray Diffraction 2.7609 2.85 -- 139 2673 0.207 0.2473 -- 100.0
X Ray Diffraction 2.85 2.9518 -- 151 2669 0.2054 0.2652 -- 99.0
X Ray Diffraction 2.9518 3.07 -- 132 2668 0.2011 0.257 -- 99.0
X Ray Diffraction 3.07 3.2097 -- 156 2662 0.192 0.261 -- 99.0
X Ray Diffraction 3.2097 3.3788 -- 139 2688 0.1902 0.2953 -- 99.0
X Ray Diffraction 3.3788 3.5904 -- 116 2693 0.1721 0.226 -- 99.0
X Ray Diffraction 3.5904 3.8675 -- 138 2717 0.1569 0.2124 -- 99.0
X Ray Diffraction 3.8675 4.2564 -- 116 2727 0.1429 0.147 -- 99.0
X Ray Diffraction 4.2564 4.8715 -- 167 2734 0.1357 0.1654 -- 100.0
X Ray Diffraction 4.8715 6.1348 -- 169 2724 0.1643 0.1723 -- 100.0
X Ray Diffraction 6.1348 43.2272 -- 135 2884 0.1683 0.1856 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.0296
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.243
f_plane_restr 0.005
f_chiral_restr 0.078
f_angle_d 1.128
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7083
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 571

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
d*TREK Data Reduction (intensity integration)
d*TREK Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
D*trek version: 9.9.8.8D data reduction
D*trek version: 9.9.8.8D data collection