X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details 12% PEG 8000, 0.1 M MES, 0.2 Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.26 α = 90
b = 119.35 β = 91.64
c = 148.03 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2013-01-28
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25

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
2.55 39.3 99.9 0.063 -- -- 4.9 -- 84020 -- -- --
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)
2.55 2.559 99.8 0.617 -- 2.5 4.8 --

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 2.55 35.334 -- 1.34 -- 83990 4149 99.85 -- 0.1704 0.1682 0.2109 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 2.55 2.579 -- 138 2631 0.2615 0.3017 -- 100.0
X Ray Diffraction 2.579 2.6093 -- 132 2672 0.266 0.3105 -- 100.0
X Ray Diffraction 2.6093 2.6411 -- 120 2686 0.2574 0.3434 -- 100.0
X Ray Diffraction 2.6411 2.6745 -- 133 2621 0.2482 0.2896 -- 100.0
X Ray Diffraction 2.6745 2.7097 -- 127 2675 0.2391 0.2867 -- 100.0
X Ray Diffraction 2.7097 2.7468 -- 149 2676 0.2271 0.2746 -- 100.0
X Ray Diffraction 2.7468 2.7861 -- 126 2619 0.2183 0.2969 -- 100.0
X Ray Diffraction 2.7861 2.8276 -- 131 2654 0.2089 0.2686 -- 100.0
X Ray Diffraction 2.8276 2.8718 -- 133 2709 0.203 0.2614 -- 100.0
X Ray Diffraction 2.8718 2.9188 -- 122 2623 0.1958 0.2495 -- 100.0
X Ray Diffraction 2.9188 2.9692 -- 166 2658 0.2031 0.2468 -- 100.0
X Ray Diffraction 2.9692 3.0231 -- 124 2647 0.1964 0.2541 -- 100.0
X Ray Diffraction 3.0231 3.0812 -- 152 2663 0.2003 0.2027 -- 100.0
X Ray Diffraction 3.0812 3.1441 -- 116 2640 0.211 0.2507 -- 100.0
X Ray Diffraction 3.1441 3.2124 -- 145 2685 0.2071 0.273 -- 100.0
X Ray Diffraction 3.2124 3.2871 -- 132 2651 0.191 0.2567 -- 100.0
X Ray Diffraction 3.2871 3.3692 -- 140 2658 0.1801 0.2479 -- 100.0
X Ray Diffraction 3.3692 3.4602 -- 128 2632 0.1798 0.2332 -- 100.0
X Ray Diffraction 3.4602 3.562 -- 154 2682 0.1697 0.2368 -- 100.0
X Ray Diffraction 3.562 3.6768 -- 135 2647 0.166 0.2228 -- 100.0
X Ray Diffraction 3.6768 3.8081 -- 150 2666 0.1597 0.2249 -- 100.0
X Ray Diffraction 3.8081 3.9604 -- 150 2635 0.1507 0.1796 -- 100.0
X Ray Diffraction 3.9604 4.1404 -- 124 2695 0.1366 0.1622 -- 100.0
X Ray Diffraction 4.1404 4.3583 -- 140 2643 0.1375 0.1699 -- 100.0
X Ray Diffraction 4.3583 4.6308 -- 137 2690 0.1273 0.1764 -- 100.0
X Ray Diffraction 4.6308 4.9874 -- 129 2659 0.1325 0.1701 -- 100.0
X Ray Diffraction 4.9874 5.4876 -- 164 2630 0.1445 0.1898 -- 100.0
X Ray Diffraction 5.4876 6.2779 -- 139 2699 0.1668 0.2187 -- 100.0
X Ray Diffraction 6.2779 7.8949 -- 166 2659 0.1675 0.2086 -- 100.0
X Ray Diffraction 7.8949 35.3376 -- 147 2736 0.1478 0.1563 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.081
f_dihedral_angle_d 17.24
f_angle_d 1.192
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13909
Nucleic Acid Atoms 1256
Heterogen Atoms 169
Solvent Atoms 304

Software

Computing
Computing Package Purpose
CBASS Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_1363) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: dev_1363) refinement
PHASER model building
CBASS data collection