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 = 157.13 α = 90
b = 157.13 β = 90
c = 211.09 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
3.1 50 99.3 0.102 0.102 -- 4.5 55483 55095 0.0 -3.0 90.1
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)
3.1 3.21 98.8 0.84 0.84 1.43 4.1 5432

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 3.35 41.674 -- 1.34 -- 43537 4348 99.28 -- 0.1825 0.1774 0.2279 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 3.35 3.3881 -- 136 1242 0.2341 0.2956 -- 100.0
X Ray Diffraction 3.3881 3.4279 -- 156 1311 0.2191 0.2798 -- 99.0
X Ray Diffraction 3.4279 3.4697 -- 159 1260 0.2017 0.2983 -- 99.0
X Ray Diffraction 3.4697 3.5136 -- 146 1322 0.2123 0.2743 -- 100.0
X Ray Diffraction 3.5136 3.5598 -- 128 1296 0.1987 0.2783 -- 99.0
X Ray Diffraction 3.5598 3.6085 -- 144 1279 0.2011 0.2658 -- 100.0
X Ray Diffraction 3.6085 3.6601 -- 143 1320 0.199 0.2313 -- 99.0
X Ray Diffraction 3.6601 3.7147 -- 147 1268 0.1943 0.2495 -- 100.0
X Ray Diffraction 3.7147 3.7727 -- 124 1315 0.1949 0.2592 -- 100.0
X Ray Diffraction 3.7727 3.8345 -- 148 1295 0.1715 0.2275 -- 100.0
X Ray Diffraction 3.8345 3.9006 -- 138 1300 0.1622 0.2445 -- 100.0
X Ray Diffraction 3.9006 3.9714 -- 129 1304 0.154 0.231 -- 100.0
X Ray Diffraction 3.9714 4.0477 -- 163 1312 0.1552 0.2295 -- 100.0
X Ray Diffraction 4.0477 4.1303 -- 146 1302 0.1542 0.2148 -- 100.0
X Ray Diffraction 4.1303 4.22 -- 143 1275 0.1464 0.2058 -- 100.0
X Ray Diffraction 4.22 4.3181 -- 150 1322 0.1462 0.1865 -- 100.0
X Ray Diffraction 4.3181 4.426 -- 136 1307 0.1463 0.201 -- 100.0
X Ray Diffraction 4.426 4.5455 -- 144 1313 0.1315 0.1875 -- 100.0
X Ray Diffraction 4.5455 4.6791 -- 155 1287 0.1282 0.1814 -- 100.0
X Ray Diffraction 4.6791 4.8299 -- 148 1312 0.1481 0.2081 -- 100.0
X Ray Diffraction 4.8299 5.0022 -- 140 1314 0.1564 0.2233 -- 100.0
X Ray Diffraction 5.0022 5.2022 -- 152 1309 0.1844 0.2692 -- 100.0
X Ray Diffraction 5.2022 5.4384 -- 142 1345 0.1905 0.2506 -- 100.0
X Ray Diffraction 5.4384 5.7245 -- 145 1319 0.2156 0.2841 -- 100.0
X Ray Diffraction 5.7245 6.0821 -- 132 1344 0.2377 0.3487 -- 100.0
X Ray Diffraction 6.0821 6.5501 -- 140 1333 0.2225 0.2931 -- 100.0
X Ray Diffraction 6.5501 7.2062 -- 153 1334 0.1796 0.2061 -- 100.0
X Ray Diffraction 7.2062 8.2419 -- 147 1342 0.1446 0.1906 -- 99.0
X Ray Diffraction 8.2419 10.3575 -- 169 1301 0.1485 0.172 -- 98.0
X Ray Diffraction 10.3575 41.6767 -- 145 1306 0.2256 0.2195 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 14.2168
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 14.2168
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -28.4337
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.075
f_dihedral_angle_d 18.242
f_angle_d 1.282
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10244
Nucleic Acid Atoms 730
Heterogen Atoms 56
Solvent Atoms 34

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: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.2_869) refinement
Phaser model building
GDE data collection