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 = 48.57 α = 90
b = 75.31 β = 93.28
c = 52.65 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
1.58 48.49 97.3 0.053 -- -- -- -- 50444 -- -3.0 20.165
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)
1.58 1.67 99.5 0.307 -- 3.1 -- --

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 1.58 48.491 -- 1.99 -- 50441 2033 97.29 -- 0.1894 0.1884 0.2132 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 1.58 1.6168 -- 133 3281 0.2371 0.2505 -- 99.0
X Ray Diffraction 1.6168 1.6572 -- 138 3280 0.2236 0.256 -- 99.0
X Ray Diffraction 1.6572 1.702 -- 139 3296 0.2218 0.2546 -- 100.0
X Ray Diffraction 1.702 1.7521 -- 137 3278 0.2107 0.2668 -- 99.0
X Ray Diffraction 1.7521 1.8086 -- 142 3248 0.2028 0.2281 -- 99.0
X Ray Diffraction 1.8086 1.8733 -- 133 3297 0.1912 0.2164 -- 99.0
X Ray Diffraction 1.8733 1.9483 -- 141 3304 0.1943 0.2348 -- 99.0
X Ray Diffraction 1.9483 2.037 -- 128 3262 0.1882 0.2141 -- 99.0
X Ray Diffraction 2.037 2.1444 -- 139 3223 0.1814 0.2117 -- 98.0
X Ray Diffraction 2.1444 2.2787 -- 142 3261 0.1782 0.2212 -- 98.0
X Ray Diffraction 2.2787 2.4546 -- 131 3212 0.1769 0.2128 -- 97.0
X Ray Diffraction 2.4546 2.7016 -- 137 3190 0.1824 0.2016 -- 96.0
X Ray Diffraction 2.7016 3.0925 -- 129 3144 0.1914 0.2072 -- 95.0
X Ray Diffraction 3.0925 3.896 -- 134 3092 0.1706 0.1824 -- 93.0
X Ray Diffraction 3.896 48.5134 -- 130 3040 0.1853 0.2018 -- 90.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.7051
Anisotropic B[1][1] 1.4008
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.7147
Anisotropic B[2][2] -0.8829
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.5179
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.267
f_plane_restr 0.005
f_chiral_restr 0.073
f_angle_d 1.256
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2724
Nucleic Acid Atoms 0
Heterogen Atoms 94
Solvent Atoms 282

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