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 = 90.03 α = 90
b = 90.03 β = 90
c = 106.66 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
1.55 62.94 100.0 0.051 -- -- -- -- 139049 -- -3.0 26.65
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)
1.55 1.65 99.9 1.047 -- 1.19 -- --

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 1.555 45.014 -- 1.36 -- 72195 2841 99.96 -- 0.1861 0.1851 0.2096 --
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 1.5549 1.5818 -- 137 3456 0.32 0.3508 -- 100.0
X Ray Diffraction 1.5818 1.6105 -- 145 3407 0.3021 0.2894 -- 100.0
X Ray Diffraction 1.6105 1.6415 -- 140 3452 0.2646 0.2777 -- 100.0
X Ray Diffraction 1.6415 1.675 -- 139 3406 0.2573 0.2498 -- 100.0
X Ray Diffraction 1.675 1.7114 -- 145 3403 0.2451 0.2719 -- 100.0
X Ray Diffraction 1.7114 1.7512 -- 138 3467 0.242 0.2801 -- 100.0
X Ray Diffraction 1.7512 1.795 -- 140 3412 0.2389 0.298 -- 100.0
X Ray Diffraction 1.795 1.8436 -- 136 3445 0.2292 0.2539 -- 100.0
X Ray Diffraction 1.8436 1.8978 -- 144 3436 0.2049 0.2212 -- 100.0
X Ray Diffraction 1.8978 1.9591 -- 136 3458 0.194 0.2241 -- 100.0
X Ray Diffraction 1.9591 2.0291 -- 147 3451 0.2025 0.2513 -- 100.0
X Ray Diffraction 2.0291 2.1103 -- 143 3459 0.1953 0.2152 -- 100.0
X Ray Diffraction 2.1103 2.2064 -- 140 3457 0.1886 0.2232 -- 100.0
X Ray Diffraction 2.2064 2.3227 -- 143 3465 0.1803 0.2011 -- 100.0
X Ray Diffraction 2.3227 2.4682 -- 144 3449 0.1776 0.2095 -- 100.0
X Ray Diffraction 2.4682 2.6588 -- 146 3505 0.1688 0.1672 -- 100.0
X Ray Diffraction 2.6588 2.9263 -- 142 3476 0.1718 0.1895 -- 100.0
X Ray Diffraction 2.9263 3.3496 -- 144 3521 0.1712 0.1676 -- 100.0
X Ray Diffraction 3.3496 4.2197 -- 142 3554 0.1642 0.2035 -- 100.0
X Ray Diffraction 4.2197 45.0329 -- 150 3675 0.1821 0.2147 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.6971
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.018
f_chiral_restr 0.141
f_dihedral_angle_d 18.822
f_plane_restr 0.011
f_angle_d 1.728
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2317
Nucleic Acid Atoms 0
Heterogen Atoms 78
Solvent Atoms 305

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