X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details 100 MM MES/IMIDAZOLE PH 6.5, 0.02 M 1,6-HEXANEDIOL, 0.02 M 1-BUTANOL, 0.02 M (RS)-1, 2-PROPANEDIOL, 0.02 M 2-PROPANOL, 0.02 M 1,4-BUTANEDIOL, 0.02 M 1,3-PROPANEDIOL, 10% (W/V) PEG 20000 AND 24% (V/V) PEG400 (USING A 2:1 RATIO OF PROTEIN TO MOTHER LIQUOR), PEPTIDE WAS AT ABOUT 50 FOLD MOLAR EXCESS

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 34.84 α = 90
b = 37.46 β = 90
c = 105.48 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2012-11-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) -- PETRA III, EMBL c/o DESY P14 (MX2)

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
1.7 37.46 98.8 0.05 -- -- 4.1 -- 15669 -- 2.7 20.34
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)
1.7 1.79 99.1 0.42 -- 2.7 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
MOLECULAR REPLACEMENT 1.7 35.298 -- 1.34 -- 15598 779 98.35 -- 0.1913 0.1896 0.2257 --
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 1.7 1.8065 -- 123 2426 0.2398 0.2697 -- 99.0
X Ray Diffraction 1.8065 1.946 -- 133 2418 0.1918 0.2502 -- 98.0
X Ray Diffraction 1.946 2.1418 -- 135 2422 0.1739 0.2186 -- 99.0
X Ray Diffraction 2.1418 2.4517 -- 133 2445 0.178 0.2612 -- 98.0
X Ray Diffraction 2.4517 3.0886 -- 133 2495 0.1944 0.224 -- 99.0
X Ray Diffraction 3.0886 35.3052 -- 122 2613 0.1886 0.2061 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.081
f_bond_d 0.006
f_dihedral_angle_d 14.208
f_plane_restr 0.005
f_chiral_restr 0.072
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1026
Nucleic Acid Atoms 0
Heterogen Atoms 11
Solvent Atoms 84

Software

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE: 1.8_1069)
XDS data reduction
SCALA data scaling
DIMPLE phasing