X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 291.0
Details 25% PEG 1500, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.63 α = 90
b = 70.63 β = 90
c = 494.52 γ = 120
Symmetry
Space Group P 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 -- 2012-11-22
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 PHOTON FACTORY BL-17A

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
2.7 50 95.3 -- -- -- -- 72276 72276 0.0 -3.0 51.0
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)
2.7 2.8 95.5 -- -- -- -- --

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 2.7 49.117 -- 1.97 72239 72239 3629 95.24 0.2287 0.2287 0.2273 0.2554 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 2.6999 2.7354 -- 102 2577 0.351 0.3626 -- 94.0
X Ray Diffraction 2.7354 2.7729 -- 144 2673 0.3206 0.369 -- 96.0
X Ray Diffraction 2.7729 2.8125 -- 141 2669 0.2998 0.3294 -- 97.0
X Ray Diffraction 2.8125 2.8545 -- 138 2649 0.3051 0.3371 -- 95.0
X Ray Diffraction 2.8545 2.8991 -- 150 2640 0.2824 0.3189 -- 97.0
X Ray Diffraction 2.8991 2.9466 -- 151 2657 0.2986 0.3213 -- 94.0
X Ray Diffraction 2.9466 2.9974 -- 142 2612 0.2829 0.3322 -- 96.0
X Ray Diffraction 2.9974 3.0519 -- 119 2724 0.2624 0.3111 -- 95.0
X Ray Diffraction 3.0519 3.1106 -- 131 2606 0.2508 0.2683 -- 95.0
X Ray Diffraction 3.1106 3.1741 -- 150 2600 0.2282 0.2364 -- 95.0
X Ray Diffraction 3.1741 3.2431 -- 135 2604 0.2341 0.2517 -- 94.0
X Ray Diffraction 3.2431 3.3185 -- 131 2654 0.252 0.2921 -- 96.0
X Ray Diffraction 3.3185 3.4015 -- 147 2594 0.2526 0.3033 -- 93.0
X Ray Diffraction 3.4015 3.4934 -- 142 2644 0.2349 0.2807 -- 95.0
X Ray Diffraction 3.4934 3.5962 -- 139 2578 0.2311 0.2425 -- 93.0
X Ray Diffraction 3.5962 3.7122 -- 136 2611 0.2394 0.2687 -- 93.0
X Ray Diffraction 3.7122 3.8449 -- 125 2602 0.2345 0.2909 -- 97.0
X Ray Diffraction 3.8449 3.9987 -- 151 2612 0.2113 0.2257 -- 94.0
X Ray Diffraction 3.9987 4.1806 -- 146 2646 0.2083 0.2512 -- 95.0
X Ray Diffraction 4.1806 4.4009 -- 151 2679 0.205 0.234 -- 96.0
X Ray Diffraction 4.4009 4.6765 -- 155 2645 0.1944 0.2019 -- 96.0
X Ray Diffraction 4.6765 5.0372 -- 147 2666 0.1927 0.2314 -- 96.0
X Ray Diffraction 5.0372 5.5435 -- 149 2606 0.2011 0.22 -- 96.0
X Ray Diffraction 5.5435 6.3442 -- 145 2747 0.2014 0.2304 -- 99.0
X Ray Diffraction 6.3442 7.9875 -- 125 2775 0.1984 0.2106 -- 99.0
X Ray Diffraction 7.9875 49.1248 -- 137 2540 0.2124 0.2445 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 77.8937
Anisotropic B[1][1] -8.6607
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -8.6607
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 17.3213
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.136
f_dihedral_angle_d 18.767
f_angle_d 1.08
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 15480
Nucleic Acid Atoms 0
Heterogen Atoms 212
Solvent Atoms 0

Software

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