X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details 25% PEG 2000 MME, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.51 α = 90
b = 70.51 β = 90
c = 489.56 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 315r -- 2012-10-03
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 1.0000 SSRF BL17U

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 50 90.6 -- -- -- -- 85842 85842 0.0 -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)
2.5 2.59 81.5 -- -- -- -- --

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 2.502 48.887 -- 1.96 85804 85804 4284 91.21 0.2377 0.2377 0.2355 0.2793 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 2.502 2.5304 -- 105 2339 0.3067 0.3616 -- 77.0
X Ray Diffraction 2.5304 2.5602 -- 134 2745 0.3001 0.3285 -- 94.0
X Ray Diffraction 2.5602 2.5914 -- 144 2878 0.2984 0.3782 -- 93.0
X Ray Diffraction 2.5914 2.6242 -- 172 2748 0.2827 0.3351 -- 94.0
X Ray Diffraction 2.6242 2.6587 -- 141 2763 0.289 0.3646 -- 94.0
X Ray Diffraction 2.6587 2.6951 -- 126 2849 0.2686 0.3231 -- 94.0
X Ray Diffraction 2.6951 2.7336 -- 136 2815 0.2705 0.3401 -- 94.0
X Ray Diffraction 2.7336 2.7744 -- 144 2790 0.2759 0.314 -- 95.0
X Ray Diffraction 2.7744 2.8178 -- 172 2835 0.2819 0.344 -- 93.0
X Ray Diffraction 2.8178 2.864 -- 152 2722 0.2614 0.3348 -- 95.0
X Ray Diffraction 2.864 2.9134 -- 158 2830 0.2658 0.3159 -- 94.0
X Ray Diffraction 2.9134 2.9663 -- 141 2797 0.2564 0.314 -- 94.0
X Ray Diffraction 2.9663 3.0234 -- 147 2744 0.2668 0.2843 -- 93.0
X Ray Diffraction 3.0234 3.0851 -- 117 2802 0.2562 0.3378 -- 93.0
X Ray Diffraction 3.0851 3.1521 -- 150 2736 0.2543 0.3159 -- 93.0
X Ray Diffraction 3.1521 3.2255 -- 176 2750 0.2498 0.312 -- 91.0
X Ray Diffraction 3.2255 3.3061 -- 137 2723 0.2519 0.2867 -- 92.0
X Ray Diffraction 3.3061 3.3955 -- 145 2772 0.2438 0.3087 -- 91.0
X Ray Diffraction 3.3955 3.4954 -- 136 2681 0.2472 0.2483 -- 91.0
X Ray Diffraction 3.4954 3.6081 -- 148 2658 0.2186 0.2754 -- 91.0
X Ray Diffraction 3.6081 3.7371 -- 147 2753 0.222 0.2674 -- 90.0
X Ray Diffraction 3.7371 3.8866 -- 130 2649 0.216 0.2807 -- 89.0
X Ray Diffraction 3.8866 4.0634 -- 126 2695 0.2012 0.2487 -- 91.0
X Ray Diffraction 4.0634 4.2776 -- 159 2629 0.1985 0.2471 -- 90.0
X Ray Diffraction 4.2776 4.5454 -- 156 2659 0.2009 0.2197 -- 88.0
X Ray Diffraction 4.5454 4.896 -- 130 2635 0.195 0.2522 -- 88.0
X Ray Diffraction 4.896 5.3882 -- 150 2639 0.2143 0.2609 -- 89.0
X Ray Diffraction 5.3882 6.1665 -- 117 2643 0.2216 0.2342 -- 89.0
X Ray Diffraction 6.1665 7.7642 -- 147 2689 0.2324 0.2435 -- 89.0
X Ray Diffraction 7.7642 48.8967 -- 141 2552 0.2313 0.2537 -- 86.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.2871
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.078
f_dihedral_angle_d 16.858
f_angle_d 1.137
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 15476
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 373

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: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
PHASER model building
ADSC version: Quantum data collection