X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 277.0
Details 0.1 M sodium acetate, pH 4.5, 30% (w/v) PEG-6000, 0.3 M LiSO4, 3% (w/v) TMAO, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide, vapor diffusion, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.58 α = 90
b = 75.59 β = 93.13
c = 52.6 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2010-12-09
Diffraction Radiation
Monochromator Protocol
two flat Si(111) crystals, mounted in a model DCM from Khozu SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.116 ALS 8.3.1

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
1.69 48.51 98.8 0.056 -- -- -- -- 42023 -- -3.0 21.041
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)
1.69 1.78 99.4 0.326 -- 3.02 -- --

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 1.69 48.508 -- 1.99 -- 42019 1677 98.77 -- 0.1699 0.1689 0.1957 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 1.69 1.7398 -- 137 3393 0.2283 0.284 -- 100.0
X Ray Diffraction 1.7398 1.7959 -- 141 3341 0.212 0.2563 -- 99.0
X Ray Diffraction 1.7959 1.8601 -- 138 3358 0.1915 0.2277 -- 100.0
X Ray Diffraction 1.8601 1.9346 -- 146 3391 0.1766 0.2167 -- 99.0
X Ray Diffraction 1.9346 2.0226 -- 137 3365 0.1659 0.2078 -- 99.0
X Ray Diffraction 2.0226 2.1293 -- 139 3343 0.1544 0.181 -- 99.0
X Ray Diffraction 2.1293 2.2627 -- 140 3369 0.1544 0.2012 -- 99.0
X Ray Diffraction 2.2627 2.4374 -- 143 3366 0.1578 0.1935 -- 99.0
X Ray Diffraction 2.4374 2.6826 -- 140 3372 0.1638 0.1919 -- 99.0
X Ray Diffraction 2.6826 3.0708 -- 138 3367 0.1766 0.208 -- 98.0
X Ray Diffraction 3.0708 3.8686 -- 138 3312 0.1631 0.1684 -- 97.0
X Ray Diffraction 3.8686 48.5275 -- 140 3365 0.1601 0.1704 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.7495
Anisotropic B[1][1] -0.5595
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.2052
Anisotropic B[2][2] -0.8355
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.395
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.503
f_plane_restr 0.006
f_chiral_restr 0.089
f_angle_d 1.397
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2748
Nucleic Acid Atoms 0
Heterogen Atoms 83
Solvent Atoms 355

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
XSCALE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction