X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details PEG 8000, sodium cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.18 α = 90
b = 78.91 β = 106.13
c = 85.81 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
-- -- -- 2011-02-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.976300 ESRF ID23-1

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
2 82.43 97.5 -- 0.074 -- 2.3 40762 40762 -- -- --
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)
2.0 2.11 96.8 0.285 0.285 2.0 2.3 5892

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 2.0 41.216 -- 1.33 40762 40605 4068 97.15 -- 0.248 0.2448 0.2773 --
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 2.0 2.0236 -- 155 1242 0.3117 0.4036 -- 99.0
X Ray Diffraction 2.0236 2.0482 -- 126 1319 0.3394 0.3633 -- 99.0
X Ray Diffraction 2.0482 2.0742 -- 147 1199 0.3545 0.4049 -- 94.0
X Ray Diffraction 2.0742 2.1014 -- 120 1186 0.3806 0.4379 -- 90.0
X Ray Diffraction 2.1014 2.1302 -- 117 1248 0.3212 0.3549 -- 99.0
X Ray Diffraction 2.1302 2.1607 -- 134 1285 0.3197 0.3451 -- 98.0
X Ray Diffraction 2.1607 2.1929 -- 144 1311 0.3082 0.3318 -- 98.0
X Ray Diffraction 2.1929 2.2272 -- 147 1213 0.314 0.3697 -- 98.0
X Ray Diffraction 2.2272 2.2637 -- 137 1195 0.3563 0.3781 -- 92.0
X Ray Diffraction 2.2637 2.3027 -- 152 1228 0.3265 0.3838 -- 96.0
X Ray Diffraction 2.3027 2.3446 -- 141 1240 0.2832 0.3733 -- 98.0
X Ray Diffraction 2.3446 2.3897 -- 136 1308 0.2632 0.3305 -- 98.0
X Ray Diffraction 2.3897 2.4384 -- 168 1235 0.2783 0.3288 -- 99.0
X Ray Diffraction 2.4384 2.4915 -- 130 1264 0.2596 0.3441 -- 98.0
X Ray Diffraction 2.4915 2.5494 -- 143 1276 0.2606 0.2985 -- 98.0
X Ray Diffraction 2.5494 2.6132 -- 137 1256 0.2552 0.3012 -- 98.0
X Ray Diffraction 2.6132 2.6838 -- 125 1281 0.2726 0.2905 -- 98.0
X Ray Diffraction 2.6838 2.7628 -- 125 1271 0.2689 0.2903 -- 98.0
X Ray Diffraction 2.7628 2.8519 -- 138 1290 0.2566 0.2799 -- 97.0
X Ray Diffraction 2.8519 2.9538 -- 158 1257 0.2398 0.2848 -- 99.0
X Ray Diffraction 2.9538 3.072 -- 145 1265 0.2358 0.2579 -- 97.0
X Ray Diffraction 3.072 3.2118 -- 144 1240 0.2443 0.2939 -- 96.0
X Ray Diffraction 3.2118 3.3811 -- 144 1253 0.2362 0.2581 -- 98.0
X Ray Diffraction 3.3811 3.5928 -- 170 1241 0.2362 0.2442 -- 97.0
X Ray Diffraction 3.5928 3.87 -- 133 1279 0.2088 0.2442 -- 98.0
X Ray Diffraction 3.87 4.2591 -- 135 1280 0.1933 0.2101 -- 97.0
X Ray Diffraction 4.2591 4.8745 -- 133 1305 0.1657 0.1667 -- 98.0
X Ray Diffraction 4.8745 6.1382 -- 135 1331 0.18 0.1987 -- 99.0
X Ray Diffraction 6.1382 41.2248 -- 149 1239 0.2017 0.2221 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.902
Anisotropic B[1][1] -1.3602
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 5.5002
Anisotropic B[2][2] -5.3994
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.7596
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.983
f_plane_restr 0.008
f_chiral_restr 0.087
f_angle_d 1.244
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4708
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 254

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
SCALA version: 3.3.16 data reduction
Mosflm data collection