X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 277.0
Details 3 mM TCEP, 0.1 M sodium citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.68 α = 90
b = 152.04 β = 94.54
c = 96.05 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-06-12
Diffraction Radiation
Monochromator Protocol
Si mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E

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
2.6 50 97.9 -- 0.096 -- 2.7 78812 77126 -3.0 -1.0 --
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)
2.6 2.69 98.0 -- 0.474 1.9 2.5 --

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 2.6 39.47 -- 1.38 78812 77070 3882 97.8 -- 0.198 0.196 0.246 --
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 2.6 2.6308 -- 136 2524 0.2997 0.3395 -- 95.0
X Ray Diffraction 2.6308 2.6641 -- 151 2588 0.3091 0.3539 -- 98.0
X Ray Diffraction 2.6641 2.6991 -- 126 2623 0.2891 0.4005 -- 99.0
X Ray Diffraction 2.6991 2.7361 -- 143 2647 0.2897 0.3441 -- 98.0
X Ray Diffraction 2.7361 2.7752 -- 138 2596 0.2644 0.3441 -- 99.0
X Ray Diffraction 2.7752 2.8166 -- 132 2648 0.2604 0.3374 -- 98.0
X Ray Diffraction 2.8166 2.8606 -- 147 2609 0.2602 0.328 -- 99.0
X Ray Diffraction 2.8606 2.9075 -- 120 2659 0.254 0.2948 -- 98.0
X Ray Diffraction 2.9075 2.9576 -- 132 2614 0.2426 0.3451 -- 99.0
X Ray Diffraction 2.9576 3.0114 -- 144 2634 0.2205 0.289 -- 99.0
X Ray Diffraction 3.0114 3.0692 -- 137 2610 0.2088 0.2925 -- 98.0
X Ray Diffraction 3.0692 3.1319 -- 143 2610 0.2033 0.2318 -- 98.0
X Ray Diffraction 3.1319 3.1999 -- 148 2656 0.1998 0.251 -- 99.0
X Ray Diffraction 3.1999 3.2743 -- 121 2633 0.19 0.2174 -- 99.0
X Ray Diffraction 3.2743 3.3562 -- 118 2650 0.1931 0.2169 -- 99.0
X Ray Diffraction 3.3562 3.4469 -- 125 2652 0.1928 0.2736 -- 98.0
X Ray Diffraction 3.4469 3.5482 -- 152 2625 0.1969 0.2537 -- 99.0
X Ray Diffraction 3.5482 3.6627 -- 148 2599 0.1946 0.2521 -- 98.0
X Ray Diffraction 3.6627 3.7935 -- 145 2633 0.1834 0.2319 -- 98.0
X Ray Diffraction 3.7935 3.9453 -- 146 2626 0.1698 0.2288 -- 98.0
X Ray Diffraction 3.9453 4.1246 -- 142 2628 0.1523 0.2223 -- 98.0
X Ray Diffraction 4.1246 4.3418 -- 148 2611 0.1482 0.1874 -- 98.0
X Ray Diffraction 4.3418 4.6135 -- 155 2586 0.1419 0.1879 -- 97.0
X Ray Diffraction 4.6135 4.9691 -- 126 2623 0.1502 0.1909 -- 97.0
X Ray Diffraction 4.9691 5.4679 -- 160 2561 0.1741 0.2289 -- 96.0
X Ray Diffraction 5.4679 6.2565 -- 130 2573 0.1995 0.2078 -- 96.0
X Ray Diffraction 6.2565 7.8722 -- 146 2583 0.2136 0.2707 -- 96.0
X Ray Diffraction 7.8722 39.467 -- 123 2587 0.1703 0.1829 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 12.3146
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.4507
Anisotropic B[2][2] -6.5241
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.7905
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.088
f_dihedral_angle_d 17.534
f_angle_d 1.19
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13152
Nucleic Acid Atoms 978
Heterogen Atoms 69
Solvent Atoms 860

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
PHASER model building
MAR345dtb data collection