X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details 40% MPD, SPERMINE, MAGNESIUM CHLORIDE, SODIUM CACODYLATE PH 7.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 25.3 α = 90
b = 40.27 β = 90
c = 64.88 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL (PILATUS 2M) DECTRIS MIRRORS 2011-07-24
Diffraction Radiation
Monochromator Protocol
SI (111) DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 -- DIAMOND I04-1

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
1.21 34.22 95.8 0.02 -- -- 5.3 -- 19814 -- 1.0 15.58
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)
1.21 1.24 79.4 0.52 -- 2.4 4.3 --

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 1.3 34.2 -- 0.0 -- 17362 2971 93.78 -- 0.1452 0.1421 0.1734 --
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 1.3 1.3213 -- 130 1167 0.1948 0.2261 -- 84.0
X Ray Diffraction 1.3213 1.3441 -- 121 1149 0.1855 0.2134 -- 85.0
X Ray Diffraction 1.3441 1.3685 -- 136 1180 0.1809 0.2285 -- 89.0
X Ray Diffraction 1.3685 1.3949 -- 137 1240 0.1621 0.2393 -- 91.0
X Ray Diffraction 1.3949 1.4233 -- 135 1214 0.1664 0.2242 -- 92.0
X Ray Diffraction 1.4233 1.4543 -- 142 1259 0.1503 0.2022 -- 94.0
X Ray Diffraction 1.4543 1.4881 -- 147 1296 0.1595 0.2397 -- 94.0
X Ray Diffraction 1.4881 1.5253 -- 139 1201 0.1401 0.1885 -- 91.0
X Ray Diffraction 1.5253 1.5666 -- 141 1300 0.1195 0.1947 -- 96.0
X Ray Diffraction 1.5666 1.6127 -- 146 1291 0.1129 0.1627 -- 95.0
X Ray Diffraction 1.6127 1.6647 -- 144 1284 0.1001 0.1261 -- 95.0
X Ray Diffraction 1.6647 1.7242 -- 142 1299 0.0979 0.1537 -- 97.0
X Ray Diffraction 1.7242 1.7932 -- 149 1330 0.1065 0.1331 -- 97.0
X Ray Diffraction 1.7932 1.8749 -- 146 1312 0.1243 0.1795 -- 98.0
X Ray Diffraction 1.8749 1.9737 -- 147 1322 0.1294 0.1921 -- 98.0
X Ray Diffraction 1.9737 2.0973 -- 141 1237 0.1325 0.1572 -- 92.0
X Ray Diffraction 2.0973 2.2592 -- 148 1318 0.1357 0.1952 -- 98.0
X Ray Diffraction 2.2592 2.4865 -- 146 1324 0.1655 0.2007 -- 97.0
X Ray Diffraction 2.4865 2.8462 -- 149 1300 0.1505 0.1917 -- 97.0
X Ray Diffraction 2.8462 3.5853 -- 141 1286 0.1645 0.1664 -- 95.0
X Ray Diffraction 3.5853 34.2269 -- 144 1288 0.1385 0.1432 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.06
Anisotropic B[1][1] 7.7695
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.7934
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.9761
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.041
f_chiral_restr 0.124
f_dihedral_angle_d 30.11
f_angle_d 2.486
f_bond_d 0.022
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 490
Heterogen Atoms 1
Solvent Atoms 136

Software

Computing
Computing Package Purpose
XIA2 Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE) refinement
PHASER model building