X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Details VAPOR DIFFUSION METHOD RESERVOIR SOLUTION: 18% (W/V) PEG 6K, 100 MM AMMONIUM CITRATE 5MM CACL2, 10MM DTT, 2% (V/V) 1,4-DIOXANE PROTEIN SOLUTION: 7.3 MG/ML PROTEIN (50 MM TRIS-HCL [PH 7.5]) EACH 4 UL WAS MIXED FOR DROPLET

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.5 α = 90
b = 56.5 β = 90
c = 233.4 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A -- Photon Factory BL-6A

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 40 95.1 0.085 -- -- 4.0 -- 77899 -- -- --

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
MIRAS 2.3 6.0 -- 2.0 -- 17811 -- 95.1 -- -- 0.204 0.289 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 2.3 2.4 -- -- 1852 0.2776 0.3278 -- --
RMS Deviations
Key Refinement Restraint Deviation
x_angle_deg 1.613
x_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3296
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 99

Software

Software
Software Name Purpose
WEIS data collection
ROTAVATA-AGROVATA data reduction
PHASES phasing
X-PLOR refinement version: 3.1
WEIS data reduction
CCP4 data scaling version: (AGROVATA
ROTAVATA) data scaling