X-RAY DIFFRACTION Experimental Data & Validation


Lost? View more X-Ray Crystallographic info.

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 5.4
Temperature 277.0
Details 100 mM sodium citrate pH 5.4, 200 mM magnesium acetate, and 12% w/v polyethylene glycol 5,000 mono methyl ether, VAPOR DIFFUSION, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 321.85 α = 90
b = 95.26 β = 102.01
c = 79.01 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2013-06-05
Diffraction Radiation
Monochromator Protocol
Liquid nitrogen-cooled double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.9762 SSRL BL12-2

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
2.5 40 98.7 -- -- -- -- -- 79820 -- -- --

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 2.5 39.736 -- 1.33 -- 79384 3959 98.05 -- 0.2035 0.2021 0.2309 PHENIX
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 2.5 2.5305 2546 149 2546 0.4664 0.4581 -- 93.0
X Ray Diffraction 2.5305 2.5625 2664 137 2664 0.4231 0.4705 -- 97.0
X Ray Diffraction 2.5625 2.5963 2646 136 2646 0.3853 0.4037 -- 98.0
X Ray Diffraction 2.5963 2.6318 2697 140 2697 0.3616 0.3968 -- 97.0
X Ray Diffraction 2.6318 2.6694 2616 148 2616 0.3462 0.3781 -- 98.0
X Ray Diffraction 2.6694 2.7092 2712 162 2712 0.32 0.34 -- 98.0
X Ray Diffraction 2.7092 2.7516 2713 128 2713 0.3023 0.3177 -- 98.0
X Ray Diffraction 2.7516 2.7967 2630 129 2630 0.2982 0.3379 -- 96.0
X Ray Diffraction 2.7967 2.8449 2630 135 2630 0.2994 0.3612 -- 97.0
X Ray Diffraction 2.8449 2.8966 2701 165 2701 0.2729 0.3331 -- 99.0
X Ray Diffraction 2.8966 2.9523 2725 125 2725 0.2632 0.2977 -- 99.0
X Ray Diffraction 2.9523 3.0125 2690 147 2690 0.2498 0.2786 -- 99.0
X Ray Diffraction 3.0125 3.078 2751 144 2751 0.258 0.3248 -- 99.0
X Ray Diffraction 3.078 3.1496 2686 144 2686 0.2523 0.305 -- 99.0
X Ray Diffraction 3.1496 3.2283 2700 135 2700 0.2493 0.2587 -- 99.0
X Ray Diffraction 3.2283 3.3156 2676 136 2676 0.2226 0.2747 -- 98.0
X Ray Diffraction 3.3156 3.4131 2699 141 2699 0.2076 0.2522 -- 98.0
X Ray Diffraction 3.4131 3.5232 2626 145 2626 0.2032 0.2303 -- 97.0
X Ray Diffraction 3.5232 3.649 2732 160 2732 0.1875 0.2219 -- 99.0
X Ray Diffraction 3.649 3.795 2725 137 2725 0.1709 0.2253 -- 100.0
X Ray Diffraction 3.795 3.9676 2764 128 2764 0.1657 0.1933 -- 99.0
X Ray Diffraction 3.9676 4.1765 2719 135 2719 0.1658 0.222 -- 99.0
X Ray Diffraction 4.1765 4.4379 2661 152 2661 0.1597 0.2076 -- 97.0
X Ray Diffraction 4.4379 4.78 2678 155 2678 0.1538 0.1811 -- 97.0
X Ray Diffraction 4.78 5.2601 2761 131 2761 0.1515 0.152 -- 99.0
X Ray Diffraction 5.2601 6.019 2762 131 2762 0.1851 0.198 -- 100.0
X Ray Diffraction 6.019 7.5747 2707 135 2707 0.1967 0.1946 -- 97.0
X Ray Diffraction 7.5747 39.7411 2808 149 2808 0.1816 0.2053 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.076
f_dihedral_angle_d 14.76
f_angle_d 1.222
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9303
Nucleic Acid Atoms 0
Heterogen Atoms 124
Solvent Atoms 246

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
XDS Data Reduction (intensity integration)
AIMLESS Data Reduction (data scaling)
REFMAC5 (rigid body) Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.2_1309) refinement
REFMAC5 version: (rigid body) model building
BLU-ICE data collection