X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.2
Temperature 298.0
Details 23% PEG3350, 0.1M BIS-TRIS pH 6.2, 0.2M K-SCN; 20% PEG400 used for cryoprotection

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.52 α = 90
b = 71.27 β = 90
c = 109.98 γ = 90
Symmetry
Space Group P 21 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2015-06-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.954 PETRA III, EMBL c/o DESY P13 (MX1)

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
1.22 49.39 99.79 0.0471 -- -- 5.4 -- 159860 -- -- 14.15
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)
1.22 1.264 99.75 1.129 -- -- 5.4 --

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 1.22 49.39 -- 1.36 -- 159854 7993 99.79 -- 0.1367 0.1357 0.1567 --
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 1.22 1.23 -- 262 4972 0.263 0.2766 -- 99.49
X Ray Diffraction 1.23 1.25 -- 265 5029 0.2515 0.2913 -- 99.81
X Ray Diffraction 1.25 1.26 -- 263 5005 0.2365 0.242 -- 99.68
X Ray Diffraction 1.26 1.28 -- 261 4949 0.222 0.228 -- 99.66
X Ray Diffraction 1.28 1.3 -- 268 5089 0.2109 0.2255 -- 99.68
X Ray Diffraction 1.3 1.31 -- 261 4971 0.209 0.2568 -- 99.83
X Ray Diffraction 1.31 1.33 -- 265 5029 0.1944 0.2292 -- 99.81
X Ray Diffraction 1.33 1.35 -- 265 5028 0.1875 0.1982 -- 99.91
X Ray Diffraction 1.35 1.37 -- 265 5035 0.1751 0.218 -- 99.87
X Ray Diffraction 1.37 1.4 -- 265 5047 0.1786 0.1939 -- 99.96
X Ray Diffraction 1.4 1.42 -- 262 4978 0.1595 0.193 -- 99.94
X Ray Diffraction 1.42 1.45 -- 264 5035 0.1514 0.1996 -- 99.92
X Ray Diffraction 1.45 1.47 -- 266 5042 0.1352 0.1738 -- 99.96
X Ray Diffraction 1.47 1.5 -- 266 5057 0.118 0.1581 -- 99.98
X Ray Diffraction 1.5 1.54 -- 264 5017 0.112 0.1469 -- 99.94
X Ray Diffraction 1.54 1.57 -- 267 5069 0.1072 0.1408 -- 99.96
X Ray Diffraction 1.57 1.61 -- 264 5024 0.1026 0.14 -- 99.89
X Ray Diffraction 1.61 1.66 -- 268 5071 0.1064 0.1476 -- 99.91
X Ray Diffraction 1.66 1.7 -- 267 5072 0.1072 0.1368 -- 99.98
X Ray Diffraction 1.7 1.76 -- 266 5060 0.112 0.151 -- 100.0
X Ray Diffraction 1.76 1.82 -- 267 5069 0.1061 0.1369 -- 99.98
X Ray Diffraction 1.82 1.9 -- 267 5082 0.1135 0.1369 -- 99.89
X Ray Diffraction 1.9 1.98 -- 267 5057 0.1156 0.148 -- 99.76
X Ray Diffraction 1.98 2.09 -- 268 5088 0.1148 0.1467 -- 99.93
X Ray Diffraction 2.09 2.22 -- 268 5090 0.112 0.1408 -- 99.94
X Ray Diffraction 2.22 2.39 -- 268 5115 0.1182 0.1409 -- 99.91
X Ray Diffraction 2.39 2.63 -- 270 5125 0.1272 0.1482 -- 99.74
X Ray Diffraction 2.63 3.01 -- 270 5138 0.1419 0.1604 -- 99.39
X Ray Diffraction 3.01 3.79 -- 272 5155 0.1383 0.1445 -- 98.82
X Ray Diffraction 3.79 49.44 -- 282 5363 0.1456 0.1481 -- 99.14
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.71
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.0895
f_bond_d 0.0109
f_plane_restr 0.0087
f_dihedral_angle_d 14.4694
f_angle_d 1.167
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3719
Nucleic Acid Atoms 0
Heterogen Atoms 66
Solvent Atoms 445

Software

Software
Software Name Purpose
PHENIX refinement version: 1.13_2998
XDS data reduction
XSCALE data scaling
PHASER phasing