X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Liquid Diffusion
pH 6.5
Temperature 304.0
Details 50mM sodium cacodylate, 7% isopropanol, pH 6.5, LIQUID DIFFUSION, temperature 304K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 157.83 α = 90
b = 157.83 β = 90
c = 211.15 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2010-09-26
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 DIAMOND I03

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 99.1 0.085 0.085 -- 4.5 94010 93164 0.0 -3.0 71.22
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 95.3 0.84 0.84 1.2 3.5 8838

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 2.9 41.832 -- 1.34 67471 67471 6838 99.45 -- 0.1899 0.1857 0.2264 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 2.9 2.933 -- 218 1992 0.2806 0.3562 -- 100.0
X Ray Diffraction 2.933 2.9675 -- 219 2026 0.2641 0.3285 -- 100.0
X Ray Diffraction 2.9675 3.0036 -- 205 2026 0.247 0.3191 -- 100.0
X Ray Diffraction 3.0036 3.0417 -- 217 2011 0.2587 0.3335 -- 100.0
X Ray Diffraction 3.0417 3.0817 -- 225 1997 0.2488 0.3145 -- 100.0
X Ray Diffraction 3.0817 3.1239 -- 225 1999 0.2369 0.2939 -- 100.0
X Ray Diffraction 3.1239 3.1685 -- 221 2043 0.2287 0.2911 -- 100.0
X Ray Diffraction 3.1685 3.2158 -- 225 2029 0.2347 0.2821 -- 100.0
X Ray Diffraction 3.2158 3.266 -- 223 1977 0.2276 0.3225 -- 100.0
X Ray Diffraction 3.266 3.3195 -- 207 2026 0.2132 0.2817 -- 100.0
X Ray Diffraction 3.3195 3.3767 -- 232 2018 0.2028 0.2433 -- 100.0
X Ray Diffraction 3.3767 3.4381 -- 248 1978 0.1922 0.2461 -- 100.0
X Ray Diffraction 3.4381 3.5042 -- 232 2040 0.1888 0.2496 -- 100.0
X Ray Diffraction 3.5042 3.5757 -- 238 1998 0.1754 0.2378 -- 100.0
X Ray Diffraction 3.5757 3.6534 -- 203 2038 0.181 0.2557 -- 100.0
X Ray Diffraction 3.6534 3.7383 -- 222 2000 0.186 0.229 -- 100.0
X Ray Diffraction 3.7383 3.8318 -- 232 2041 0.175 0.2432 -- 100.0
X Ray Diffraction 3.8318 3.9353 -- 237 2010 0.1625 0.211 -- 100.0
X Ray Diffraction 3.9353 4.051 -- 221 2038 0.1616 0.1987 -- 100.0
X Ray Diffraction 4.051 4.1816 -- 223 2023 0.1576 0.211 -- 100.0
X Ray Diffraction 4.1816 4.3309 -- 222 2029 0.1526 0.1858 -- 100.0
X Ray Diffraction 4.3309 4.5041 -- 250 2012 0.1345 0.2002 -- 100.0
X Ray Diffraction 4.5041 4.7089 -- 239 2024 0.1363 0.1594 -- 100.0
X Ray Diffraction 4.7089 4.9568 -- 209 2064 0.15 0.1766 -- 100.0
X Ray Diffraction 4.9568 5.2668 -- 233 2051 0.16 0.1956 -- 100.0
X Ray Diffraction 5.2668 5.6725 -- 247 2019 0.1753 0.2061 -- 100.0
X Ray Diffraction 5.6725 6.2417 -- 231 2059 0.1872 0.2442 -- 100.0
X Ray Diffraction 6.2417 7.141 -- 250 2057 0.1778 0.2062 -- 100.0
X Ray Diffraction 7.141 8.9822 -- 240 2074 0.155 0.1669 -- 99.0
X Ray Diffraction 8.9822 41.8368 -- 244 1934 0.1854 0.1951 -- 89.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 6.8001
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.8001
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -13.6002
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.077
f_dihedral_angle_d 16.839
f_angle_d 1.221
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10338
Nucleic Acid Atoms 730
Heterogen Atoms 58
Solvent Atoms 54

Software

Computing
Computing Package Purpose
GDE Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.6.1_357) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.1_357) refinement
Phaser model building
GDE data collection