X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 293.0
Details 3-5% PEG 4K, 0.1 M sodium acetate buffer (pH 5.5), 0.1 M MgCl2, 2mM L-proline, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 132.77 α = 90
b = 132.77 β = 90
c = 134.51 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2011-10-30
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B

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
2.53 44.43 99.95 0.11 -- -- 12.0 40355 40336 0.0 0.0 --
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)
2.53 2.62 100.0 0.49 -- 4.4 12.2 40355

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 2.53 44.32 -- 1.33 40355 40336 4013 99.07 -- 0.208 0.2038 0.245 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 2.53 2.5598 -- 129 1247 0.2952 0.3862 -- 100.0
X Ray Diffraction 2.5598 2.591 -- 136 1257 0.2693 0.2943 -- 100.0
X Ray Diffraction 2.591 2.6238 -- 143 1240 0.2544 0.3232 -- 100.0
X Ray Diffraction 2.6238 2.6583 -- 137 1240 0.253 0.279 -- 100.0
X Ray Diffraction 2.6583 2.6947 -- 141 1224 0.2435 0.3198 -- 100.0
X Ray Diffraction 2.6947 2.7332 -- 136 1237 0.2386 0.2729 -- 100.0
X Ray Diffraction 2.7332 2.774 -- 140 1244 0.2572 0.3267 -- 100.0
X Ray Diffraction 2.774 2.8173 -- 137 1258 0.2374 0.3074 -- 100.0
X Ray Diffraction 2.8173 2.8635 -- 135 1248 0.239 0.3228 -- 100.0
X Ray Diffraction 2.8635 2.9129 -- 142 1242 0.2487 0.3164 -- 100.0
X Ray Diffraction 2.9129 2.9658 -- 131 1241 0.248 0.2871 -- 100.0
X Ray Diffraction 2.9658 3.0229 -- 140 1245 0.2611 0.3506 -- 100.0
X Ray Diffraction 3.0229 3.0845 -- 136 1256 0.2585 0.2959 -- 100.0
X Ray Diffraction 3.0845 3.1516 -- 143 1252 0.2579 0.3241 -- 100.0
X Ray Diffraction 3.1516 3.2249 -- 138 1249 0.241 0.295 -- 100.0
X Ray Diffraction 3.2249 3.3055 -- 140 1245 0.2331 0.2671 -- 100.0
X Ray Diffraction 3.3055 3.3948 -- 139 1262 0.2262 0.2681 -- 100.0
X Ray Diffraction 3.3948 3.4947 -- 141 1258 0.2185 0.2673 -- 100.0
X Ray Diffraction 3.4947 3.6075 -- 133 1260 0.2107 0.2311 -- 100.0
X Ray Diffraction 3.6075 3.7363 -- 134 1259 0.1955 0.2617 -- 100.0
X Ray Diffraction 3.7363 3.8858 -- 145 1259 0.1945 0.2362 -- 100.0
X Ray Diffraction 3.8858 4.0626 -- 138 1274 0.183 0.2228 -- 100.0
X Ray Diffraction 4.0626 4.2766 -- 140 1278 0.1637 0.2026 -- 100.0
X Ray Diffraction 4.2766 4.5443 -- 143 1270 0.1596 0.1787 -- 100.0
X Ray Diffraction 4.5443 4.8948 -- 140 1280 0.1595 0.2004 -- 100.0
X Ray Diffraction 4.8948 5.3866 -- 146 1296 0.1809 0.2264 -- 100.0
X Ray Diffraction 5.3866 6.1642 -- 140 1295 0.1974 0.2394 -- 100.0
X Ray Diffraction 6.1642 7.7595 -- 148 1319 0.1951 0.221 -- 100.0
X Ray Diffraction 7.7595 44.3268 -- 122 1088 0.1925 0.1991 -- 77.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.054
f_dihedral_angle_d 20.739
f_angle_d 0.928
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3539
Nucleic Acid Atoms 1224
Heterogen Atoms 0
Solvent Atoms 148

Software

Computing
Computing Package Purpose
MOSFLM Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_1352) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: dev_1352) refinement
PHASER model building
MOSFLM data collection