X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details Protein at 7.5 mg/mL in 50 mM HEPES, pH 7.0, 150 mM NaCl, 2 mM DTT was mixed with precipitant consisting of 18 - 23 percent PEG-3350, 0.2 M ammonium sulphate, 0.1 M PCTP pH 7.5 in a 1:1 ratio to give a 4 microL drop

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.33 α = 90
b = 89.63 β = 90
c = 96.25 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-10-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 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
2.87 55.17 98.4 0.109 -- -- 4.0 -- 13545 -- -- 73.96
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)
2.87 2.95 99.5 0.585 -- 2.0 4.0 --

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 2.87 55.17 -- 0.0 -- 13519 667 97.63 -- 0.1649 0.1611 0.2388 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 2.87 3.1 -- 130 2714 0.189 0.3135 -- 97.63
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 53.42
Anisotropic B[1][1] 10.898
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.6997
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -12.5977
RMS Deviations
Key Refinement Restraint Deviation
BOND LENGTHS 0.01
BOND ANGLES 1.13
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.317
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4005
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 102

Software

Software
Software Name Purpose
XDS data reduction
SCALA data scaling
BUSTER refinement version: 2.11.2
PHASER phasing