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 = 48.3 α = 90
b = 75.09 β = 93.08
c = 52.76 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 -- 2012-06-02
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
1.48 43.13 97.4 0.053 -- -- -- -- 60993 -- -3.0 21.865
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)
1.48 1.56 99.4 0.47 -- 2.24 -- --

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 1.48 43.128 -- 1.99 -- 60991 2437 97.39 -- 0.1753 0.1743 0.1981 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 1.48 1.5102 -- 150 3515 0.2378 0.273 -- 99.0
X Ray Diffraction 1.5102 1.5431 -- 139 3486 0.2228 0.2393 -- 99.0
X Ray Diffraction 1.5431 1.579 -- 145 3498 0.2098 0.2476 -- 99.0
X Ray Diffraction 1.579 1.6184 -- 147 3505 0.2019 0.2367 -- 99.0
X Ray Diffraction 1.6184 1.6622 -- 144 3503 0.1896 0.2207 -- 99.0
X Ray Diffraction 1.6622 1.7111 -- 145 3468 0.1836 0.2164 -- 99.0
X Ray Diffraction 1.7111 1.7663 -- 141 3467 0.1824 0.2238 -- 98.0
X Ray Diffraction 1.7663 1.8295 -- 145 3495 0.1731 0.2366 -- 98.0
X Ray Diffraction 1.8295 1.9027 -- 146 3455 0.1671 0.1937 -- 99.0
X Ray Diffraction 1.9027 1.9893 -- 146 3486 0.1655 0.1936 -- 98.0
X Ray Diffraction 1.9893 2.0942 -- 145 3452 0.1659 0.1962 -- 98.0
X Ray Diffraction 2.0942 2.2254 -- 142 3451 0.1619 0.1901 -- 97.0
X Ray Diffraction 2.2254 2.3972 -- 142 3400 0.1598 0.2164 -- 96.0
X Ray Diffraction 2.3972 2.6384 -- 138 3355 0.168 0.2034 -- 95.0
X Ray Diffraction 2.6384 3.0201 -- 141 3340 0.1805 0.1859 -- 94.0
X Ray Diffraction 3.0201 3.8047 -- 138 3344 0.1643 0.1819 -- 94.0
X Ray Diffraction 3.8047 43.146 -- 143 3334 0.171 0.1666 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.8111
Anisotropic B[1][1] 0.1971
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.0694
Anisotropic B[2][2] 0.3903
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.5875
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.312
f_plane_restr 0.01
f_chiral_restr 0.124
f_angle_d 1.849
f_bond_d 0.021
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2735
Nucleic Acid Atoms 0
Heterogen Atoms 82
Solvent Atoms 298

Software

Computing
Computing Package Purpose
BLU-IICE 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