X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 293.15
Details 26% PEG 4000, 0.2 M ammonium acetate, 5 mM magnesium chloride, 0.8 mM AMPPNP, 0.1 M sodium citrate pH 5.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 35.82 α = 90
b = 59.13 β = 99.02
c = 70.34 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2013-07-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.98406 ESRF ID14-4

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
2.25 45.03 99.4 -- 0.067 7.475 3.4 13806 13806 -- -- 44.28
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)
2.25 2.33 99.5 0.793 0.793 0.9 3.5 1342

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
FOURIER SYNTHESIS 2.25 45.026 -- 1.33 -- 13780 689 99.16 -- 0.2039 0.2029 0.2224 --
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 2.2501 2.4238 -- 152 2585 0.3222 0.3779 -- 99.0
X Ray Diffraction 2.4238 2.6677 -- 128 2603 0.2892 0.3334 -- 99.0
X Ray Diffraction 2.6677 3.0536 -- 130 2629 0.2351 0.2911 -- 99.0
X Ray Diffraction 3.0536 3.8469 -- 127 2641 0.2084 0.2193 -- 99.0
X Ray Diffraction 3.8469 45.0353 -- 152 2633 0.1587 0.1737 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 75.6
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.612
f_chiral_restr 0.047
f_plane_restr 0.003
f_bond_d 0.004
f_angle_d 0.758
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2288
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 22

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.20
PHENIX refinement
PDB_EXTRACT data extraction version: 3.15
XDS data reduction
REFMAC phasing