X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 277.0
Details well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.93 α = 90
b = 89.93 β = 90
c = 106.59 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
PIXEL DECTRIS PILATUS 6M -- 2016-09-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 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
1.65 77.88 99.7 0.072 -- -- -- -- 115183 -- -3.0 26.07
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)
1.65 1.75 98.4 0.976 -- 1.5 -- --

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 1.654 77.882 -- 1.37 -- 59977 2362 99.92 -- 0.1827 0.1819 0.2011 --
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 1.6536 1.6873 -- 137 3326 0.3192 0.307 -- 99.0
X Ray Diffraction 1.6873 1.724 -- 142 3360 0.2865 0.2896 -- 100.0
X Ray Diffraction 1.724 1.7641 -- 134 3375 0.2669 0.3158 -- 100.0
X Ray Diffraction 1.7641 1.8083 -- 136 3331 0.2451 0.2603 -- 100.0
X Ray Diffraction 1.8083 1.8572 -- 135 3346 0.2234 0.2176 -- 100.0
X Ray Diffraction 1.8572 1.9118 -- 141 3385 0.2048 0.2402 -- 100.0
X Ray Diffraction 1.9118 1.9735 -- 133 3346 0.2073 0.2364 -- 100.0
X Ray Diffraction 1.9735 2.0441 -- 141 3364 0.2055 0.2221 -- 100.0
X Ray Diffraction 2.0441 2.1259 -- 138 3346 0.1987 0.2561 -- 100.0
X Ray Diffraction 2.1259 2.2227 -- 139 3401 0.185 0.2239 -- 100.0
X Ray Diffraction 2.2227 2.3399 -- 139 3358 0.181 0.188 -- 100.0
X Ray Diffraction 2.3399 2.4865 -- 140 3395 0.1685 0.1981 -- 100.0
X Ray Diffraction 2.4865 2.6785 -- 143 3400 0.1645 0.1662 -- 100.0
X Ray Diffraction 2.6785 2.948 -- 141 3381 0.1707 0.1784 -- 100.0
X Ray Diffraction 2.948 3.3746 -- 136 3444 0.1685 0.1609 -- 100.0
X Ray Diffraction 3.3746 4.2516 -- 140 3463 0.1621 0.1981 -- 100.0
X Ray Diffraction 4.2516 77.9682 -- 147 3594 0.1761 0.1949 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.7238
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.011
f_dihedral_angle_d 19.62
f_bond_d 0.02
f_chiral_restr 0.271
f_angle_d 1.933
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2305
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 318

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10.1_2155
XSCALE data scaling
PHASER phasing
PDB_EXTRACT data extraction version: 3.22
XDS data reduction