X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
pH 6.5
Temperature 298.0
Details 17% MPD

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 402.1 α = 90
b = 402.1 β = 90
c = 175.1 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2017-04-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.98 SSRL BL12-2

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
3.5 39.19 100.0 -- -- -- 131.0 -- 175871 -- -- 85.3
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)
3.5 39.19 -- -- -- -- -- --

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
-- 3.5 39.19 -- 1.33 -- 175871 1142 98.2 -- 0.2475 0.2473 0.2773 --
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 3.5 3.6592 -- 123 18875 0.3693 0.3832 0.0 86.0
X Ray Diffraction 3.6592 3.852 -- 143 21925 0.3554 0.4031 0.0 100.0
X Ray Diffraction 3.852 4.0931 -- 144 22050 0.3374 0.3587 0.0 100.0
X Ray Diffraction 4.0931 4.4087 -- 144 22112 0.3139 0.3933 0.0 100.0
X Ray Diffraction 4.4087 4.8516 -- 146 22163 0.2613 0.3025 0.0 100.0
X Ray Diffraction 4.8516 5.552 -- 145 22229 0.2227 0.2659 0.0 100.0
X Ray Diffraction 5.552 6.9885 -- 147 22389 0.1882 0.2384 0.0 100.0
X Ray Diffraction 6.9885 39.1924 -- 150 22986 0.1542 0.1589 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 100.637
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.647
f_plane_restr 0.004
f_dihedral_angle_d 16.142
f_chiral_restr 0.038
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19088
Nucleic Acid Atoms 32943
Heterogen Atoms 582
Solvent Atoms 0

Software

Software
Software Name Purpose
MOSFLM data reduction
XSCALE data scaling
PHENIX refinement version: (1.11.1_2575)
PDB_EXTRACT data extraction version: 3.24
PHENIX phasing