X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 283.0
Details 20% PEG 1000, 0.1M Bis-Tris, 0.2M magnesium chloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.62 α = 90
b = 59.62 β = 90
c = 66.96 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2012-03-28
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 SSRL BL11-1

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
2.12 59.62 99.9 -- 0.076 -- 13.5 13310 13301 0.0 -- --
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)
2.124 2.24 99.9 0.016 1.583 0.5 13.8 1915

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 2.124 29.812 -- 0.0 -- 13272 654 99.74 -- 0.1805 0.1793 0.2035 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 2.124 2.288 -- 141 2503 0.2469 0.2725 -- 100.0
X Ray Diffraction 2.288 2.5181 -- 123 2501 0.214 0.2539 -- 100.0
X Ray Diffraction 2.5181 2.8822 -- 144 2513 0.2027 0.2705 -- 100.0
X Ray Diffraction 2.8822 3.6303 -- 121 2527 0.1856 0.2191 -- 100.0
X Ray Diffraction 3.6303 29.8154 -- 125 2574 0.1579 0.1639 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 55.412
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.422
f_plane_restr 0.002
f_chiral_restr 0.039
f_angle_d 0.561
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1465
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 72

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
CNS density modification
Phaser version: 2.3.0 molecular replacement
SCALA version: 3.3.16 data reduction