X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8.5
Details BM TUBR CRYSTALS WERE PRODUCED IN 500 NL TO 500 NL PROTEIN TO PRECIPITANT SITTING DROPS: 20 MG/ML BM TUBR, 100 MM TRIS-CL PH 8.5, 0.2 M SODIUM CITRATE, 15 % (V/V) PEG 400.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 179.85 α = 90
b = 179.85 β = 90
c = 114.34 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL (PILATUS 6M) DECTRIS -- 2011-03-14
Diffraction Radiation
Monochromator Protocol
GRAPHITE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 -- ESRF ID29

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 46.09 100.0 0.05 -- -- 9.9 -- 17357 -- 2.0 125.07
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 3.69 100.0 0.43 -- 4.8 10.4 --

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 3.5 46.085 -- 1.27 -- 17357 902 99.63 -- 0.1879 0.1858 0.2284 --
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 3.7192 -- 165 2740 0.2596 0.3184 -- 100.0
X Ray Diffraction 3.7192 4.0062 -- 150 2739 0.2071 0.2433 -- 100.0
X Ray Diffraction 4.0062 4.4091 -- 162 2766 0.1517 0.1894 -- 100.0
X Ray Diffraction 4.4091 5.0464 -- 146 2736 0.1571 0.1881 -- 100.0
X Ray Diffraction 5.0464 6.3553 -- 154 2739 0.2091 0.2355 -- 100.0
X Ray Diffraction 6.3553 46.0893 -- 125 2735 0.1827 0.2386 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 144.55
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.078
f_dihedral_angle_d 15.386
f_angle_d 1.324
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2184
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SHELXCDE, PHASER Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE) refinement
PHASER model building
SHELXCDE model building