X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Details 0.1M BICINE PH 9.0, 10% MPD

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 127.25 α = 90
b = 127.25 β = 90
c = 59.06 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL (PILATUS 2M) DECTRIS -- 2011-07-02
Diffraction Radiation
Monochromator Protocol
SINGLE BOUNCE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 -- DIAMOND I04-1

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
2.96 63.6 99.3 0.06 -- -- 3.7 -- 22113 -- 2.0 73.06
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)
2.96 3.04 99.9 0.57 -- 2.0 3.8 --

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
MOLECULAR REPLACEMENT 2.962 63.625 -- 1.98 -- 22113 1133 99.34 -- 0.2425 0.2396 0.2943 --
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 2.9617 3.0965 -- 144 2649 0.3033 0.3936 -- 100.0
X Ray Diffraction 3.0965 3.2598 -- 129 2674 0.2715 0.3615 -- 100.0
X Ray Diffraction 3.2598 3.464 -- 144 2612 0.2515 0.3205 -- 100.0
X Ray Diffraction 3.464 3.7314 -- 127 2638 0.2394 0.3299 -- 99.0
X Ray Diffraction 3.7314 4.1069 -- 150 2600 0.2384 0.3099 -- 99.0
X Ray Diffraction 4.1069 4.701 -- 143 2588 0.2197 0.2584 -- 98.0
X Ray Diffraction 4.701 5.9221 -- 138 2631 0.2214 0.2602 -- 100.0
X Ray Diffraction 5.9221 63.6397 -- 158 2588 0.2461 0.2829 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 73.1
Anisotropic B[1][1] -5.712
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.712
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 11.4241
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.094
f_plane_restr 0.005
f_angle_d 1.381
f_bond_d 0.009
f_dihedral_angle_d 16.141
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4851
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 2

Software

Computing
Computing Package Purpose
XIA2 Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHASER model building
PHENIX version: (PHENIX.REFINE) refinement