X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 50mM bis-Tris-HCl (pH 6.15), 3M NaCl, 1mM 1,4-diacetoxymercury-2,3-dimetoxybutane, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 127.83 α = 90
b = 127.83 β = 90
c = 169.59 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2010-02-08
CCD ADSC QUANTUM 315 -- 2009-11-07
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
double crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 PHOTON FACTORY AR-NW12A
SYNCHROTRON PAL/PLS BEAMLINE 4A 0.97951, 0.97966, 0.96 PAL/PLS 4A

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 27.83 98.58 -- -- -- -- 23338 23007 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)
2.7 2.75 100.0 -- -- -- -- --

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
MAD 2.701 27.835 -- 0.15 23056 21751 1886 94.34 -- 0.224 0.2107 0.2511 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 2.7012 2.7742 -- 121 1295 0.316 0.3601 -- 82.0
X Ray Diffraction 2.7742 2.8558 -- 124 1360 0.3086 0.3275 -- 86.0
X Ray Diffraction 2.8558 2.9478 -- 144 1538 0.2662 0.3335 -- 96.0
X Ray Diffraction 2.9478 3.0531 -- 144 1550 0.253 0.2796 -- 98.0
X Ray Diffraction 3.0531 3.1752 -- 146 1527 0.2412 0.3019 -- 96.0
X Ray Diffraction 3.1752 3.3194 -- 147 1504 0.2319 0.2496 -- 94.0
X Ray Diffraction 3.3194 3.4941 -- 141 1467 0.2129 0.2481 -- 93.0
X Ray Diffraction 3.4941 3.7126 -- 144 1544 0.2097 0.2629 -- 95.0
X Ray Diffraction 3.7126 3.9985 -- 152 1545 0.1779 0.2046 -- 96.0
X Ray Diffraction 3.9985 4.3994 -- 150 1569 0.1653 0.1939 -- 97.0
X Ray Diffraction 4.3994 5.0328 -- 152 1615 0.1482 0.1743 -- 98.0
X Ray Diffraction 5.0328 6.3285 -- 157 1643 0.2088 0.2117 -- 99.0
X Ray Diffraction 6.3285 27.8367 -- 164 1708 0.2386 0.2499 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.7844
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.7844
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.5688
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.099
f_dihedral_angle_d 16.726
f_angle_d 1.418
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2604
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 36

Software

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