X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 26% PEG 4000, 125mM sodium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 20% PEG 4000, 150mM sodium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.83 α = 70.45
b = 68.36 β = 88.16
c = 86.78 γ = 64.96
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2012-01-17
CCD RAYONIX MX-225 -- 2011-09-23
Diffraction Radiation
Monochromator Protocol
Si-111 crystal SINGLE WAVELENGTH
Si-111 crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 -- BESSY 14.1
SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1

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
2 57.81 95.9 0.178 0.113 -- 5.4 54973 72979 -3.0 -3.0 --
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)
2.0 2.11 95.1 -- -- -- -- --

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
SAD 2.2 40.675 -- 1.97 54973 54932 1371 96.15 0.1712 0.171 0.1699 0.2169 RANDOM
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 2.2 2.2786 5335 137 5335 0.2412 0.293 -- 95.0
X Ray Diffraction 2.2786 2.3699 5313 140 5315 0.2276 0.2686 -- 95.0
X Ray Diffraction 2.3699 2.4777 5311 123 5311 0.2161 0.2755 -- 96.0
X Ray Diffraction 2.4777 2.6083 5348 129 5348 0.2023 0.2755 -- 96.0
X Ray Diffraction 2.6083 2.7717 5357 155 5357 0.1898 0.2662 -- 96.0
X Ray Diffraction 2.7717 2.9857 5355 134 5355 0.1876 0.2429 -- 96.0
X Ray Diffraction 2.9857 3.286 5342 139 5342 0.17 0.2265 -- 96.0
X Ray Diffraction 3.286 3.7612 5394 144 5394 0.1564 0.2103 -- 97.0
X Ray Diffraction 3.7612 4.7376 5399 135 5399 0.1265 0.1583 -- 97.0
X Ray Diffraction 4.7376 40.6817 5405 135 5405 0.1537 0.1774 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 9.0635
Anisotropic B[1][2] -0.3947
Anisotropic B[1][3] -6.5621
Anisotropic B[2][2] -4.8668
Anisotropic B[2][3] -0.2829
Anisotropic B[3][3] -6.252
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.072
f_dihedral_angle_d 15.639
f_angle_d 1.07
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8685
Nucleic Acid Atoms 0
Heterogen Atoms 92
Solvent Atoms 646

Software

Computing
Computing Package Purpose
mxCuBE Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SHELXS Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
SHELXS model building
mxCuBE data collection