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 = 90.58 α = 90
b = 90.58 β = 90
c = 106.98 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
1.85 63.26 99.5 0.05 -- -- -- -- 83036 -- -3.0 37.83
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)
1.85 1.97 99.3 1.351 -- 1.01 -- --

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 1.853 63.259 -- 1.34 -- 42539 1676 97.49 -- 0.2075 0.2067 0.2278 --
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 1.853 1.9075 -- 142 3426 0.3532 0.395 -- 99.0
X Ray Diffraction 1.9075 1.9691 -- 108 2691 0.4319 0.4661 -- 77.0
X Ray Diffraction 1.9691 2.0395 -- 139 3429 0.284 0.3031 -- 100.0
X Ray Diffraction 2.0395 2.1211 -- 147 3461 0.2579 0.2779 -- 100.0
X Ray Diffraction 2.1211 2.2177 -- 141 3448 0.2362 0.2683 -- 100.0
X Ray Diffraction 2.2177 2.3346 -- 134 3236 0.3308 0.3749 -- 93.0
X Ray Diffraction 2.3346 2.4809 -- 144 3451 0.2269 0.2802 -- 100.0
X Ray Diffraction 2.4809 2.6724 -- 144 3493 0.2146 0.2134 -- 100.0
X Ray Diffraction 2.6724 2.9414 -- 141 3486 0.2078 0.209 -- 100.0
X Ray Diffraction 2.9414 3.367 -- 146 3517 0.202 0.2092 -- 100.0
X Ray Diffraction 3.367 4.2419 -- 140 3548 0.1755 0.2133 -- 100.0
X Ray Diffraction 4.2419 63.2957 -- 150 3677 0.1745 0.1894 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.7869
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 2.437
f_chiral_restr 0.202
f_plane_restr 0.014
f_dihedral_angle_d 21.218
f_bond_d 0.034
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2305
Nucleic Acid Atoms 0
Heterogen Atoms 78
Solvent Atoms 181

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