X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 277.0
Details 100mM magnesium acetate, 50mM 2-(N-morpholino)ethanesulfonic acid pH 5.8, 22% 2-methyl-2,4-pentanediol (MPD) , VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.66 α = 90
b = 176.42 β = 112.04
c = 93.64 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
CCD ADSC QUANTUM 315r -- 2012-03-14
Diffraction Radiation
Monochromator Protocol
Horizontally focusing single crystal monochromator (Crystal type Si(1 1 1)) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0000 NSRRC BL13B1

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 30 99.1 -- 0.085 -- 3.7 66542 65943 1.0 1.0 43.27
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 2.75 91.7 0.424 0.424 2.52 3.1 3034

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 2.696 27.49 -- 1.37 66698 65898 3340 98.8 0.1677 0.1677 0.1652 0.2154 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 2.6958 2.7343 -- 123 2208 0.27 0.3317 -- 85.0
X Ray Diffraction 2.7343 2.7751 -- 157 2481 0.2717 0.3481 -- 95.0
X Ray Diffraction 2.7751 2.8184 -- 128 2533 0.2625 0.3199 -- 97.0
X Ray Diffraction 2.8184 2.8646 -- 129 2609 0.2502 0.3131 -- 99.0
X Ray Diffraction 2.8646 2.9139 -- 142 2627 0.2363 0.299 -- 100.0
X Ray Diffraction 2.9139 2.9668 -- 129 2647 0.2226 0.3059 -- 100.0
X Ray Diffraction 2.9668 3.0238 -- 152 2629 0.2142 0.2928 -- 100.0
X Ray Diffraction 3.0238 3.0855 -- 138 2602 0.185 0.2493 -- 100.0
X Ray Diffraction 3.0855 3.1525 -- 129 2649 0.1678 0.2255 -- 100.0
X Ray Diffraction 3.1525 3.2257 -- 135 2664 0.1641 0.2188 -- 100.0
X Ray Diffraction 3.2257 3.3062 -- 147 2583 0.1614 0.2088 -- 100.0
X Ray Diffraction 3.3062 3.3955 -- 136 2659 0.1561 0.1974 -- 100.0
X Ray Diffraction 3.3955 3.4952 -- 138 2629 0.1532 0.2023 -- 100.0
X Ray Diffraction 3.4952 3.6078 -- 146 2624 0.147 0.2099 -- 100.0
X Ray Diffraction 3.6078 3.7364 -- 149 2630 0.1471 0.1874 -- 100.0
X Ray Diffraction 3.7364 3.8856 -- 136 2638 0.1451 0.1741 -- 100.0
X Ray Diffraction 3.8856 4.0619 -- 139 2644 0.1436 0.1921 -- 100.0
X Ray Diffraction 4.0619 4.2753 -- 133 2641 0.136 0.1881 -- 100.0
X Ray Diffraction 4.2753 4.5421 -- 130 2627 0.1254 0.1954 -- 100.0
X Ray Diffraction 4.5421 4.891 -- 135 2648 0.1385 0.1786 -- 100.0
X Ray Diffraction 4.891 5.3799 -- 138 2666 0.1564 0.2081 -- 100.0
X Ray Diffraction 5.3799 6.1507 -- 147 2637 0.1846 0.2195 -- 100.0
X Ray Diffraction 6.1507 7.7207 -- 140 2635 0.1752 0.2267 -- 99.0
X Ray Diffraction 7.7207 27.491 -- 164 2648 0.1493 0.1756 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 44.8366
Anisotropic B[1][1] 0.1508
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.7989
Anisotropic B[2][2] -0.0833
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.0675
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.073
f_dihedral_angle_d 17.511
f_angle_d 1.158
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10704
Nucleic Acid Atoms 820
Heterogen Atoms 66
Solvent Atoms 420

Software

Computing
Computing Package Purpose
bluice Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX (phenix.automr: 1.6.4_486) Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHENIX version: (phenix.automr: 1.6.4_486) model building
bluice data collection