X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.0
Details 0.085 M sodium acetate, 0.17 M ammonium acetate, 15 % glycerol, 25 % PEG4000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.96 α = 90
b = 93.13 β = 104.36
c = 90.8 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 RIGAKU SATURN 944 -- 2014-03-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54 -- --

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
2.3 26.82 99.1 0.178 -- -- 4.2 -- 47619 -- -- 16.59
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)
2.3 2.38 98.0 0.538 -- -- 4.2 --

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 2.3 26.82 -- 1.35 -- 47602 2401 99.08 -- 0.1803 0.1788 0.2072 --
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 2.3 2.3469 -- 147 2579 0.2061 0.2546 0.0 98.0
X Ray Diffraction 2.3469 2.3979 -- 146 2650 0.213 0.2402 0.0 98.0
X Ray Diffraction 2.3979 2.4537 -- 148 2615 0.2053 0.2634 0.0 98.0
X Ray Diffraction 2.4537 2.515 -- 138 2625 0.203 0.253 0.0 99.0
X Ray Diffraction 2.515 2.5829 -- 152 2632 0.2028 0.2381 0.0 99.0
X Ray Diffraction 2.5829 2.6589 -- 122 2674 0.1935 0.2366 0.0 99.0
X Ray Diffraction 2.6589 2.7446 -- 147 2612 0.1952 0.2223 0.0 99.0
X Ray Diffraction 2.7446 2.8426 -- 153 2632 0.1896 0.2365 0.0 99.0
X Ray Diffraction 2.8426 2.9563 -- 144 2661 0.1905 0.2226 0.0 99.0
X Ray Diffraction 2.9563 3.0906 -- 121 2689 0.1882 0.2146 0.0 99.0
X Ray Diffraction 3.0906 3.2533 -- 125 2681 0.1929 0.194 0.0 100.0
X Ray Diffraction 3.2533 3.4568 -- 127 2684 0.1836 0.2487 0.0 100.0
X Ray Diffraction 3.4568 3.723 -- 152 2687 0.1769 0.1746 0.0 100.0
X Ray Diffraction 3.723 4.0965 -- 152 2651 0.1591 0.1655 0.0 100.0
X Ray Diffraction 4.0965 4.6865 -- 142 2689 0.138 0.1679 0.0 100.0
X Ray Diffraction 4.6865 5.8942 -- 148 2688 0.1576 0.1756 0.0 100.0
X Ray Diffraction 5.8942 26.8268 -- 137 2752 0.1604 0.1964 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.3883
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.003
f_chiral_restr 0.044
f_plane_restr 0.004
f_angle_d 0.563
f_dihedral_angle_d 11.338
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7435
Nucleic Acid Atoms 0
Heterogen Atoms 49
Solvent Atoms 369

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10.1_2155
Aimless data scaling version: 0.1.29
PDB_EXTRACT data extraction version: 3.22
XDS data reduction
PHENIX phasing