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 = 48.39 α = 90
b = 75.58 β = 93.28
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 -- 2010-10-20
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
1.67 48.31 93.3 0.061 -- -- -- -- 40938 -- -3.0 19.954
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)
1.67 1.76 97.2 0.318 -- 3.06 -- --

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
PHENIX 1.67 48.311 -- 1.99 -- 40933 1636 93.26 -- 0.2062 0.2048 0.2393 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 1.67 1.7191 -- 140 3388 0.2558 0.3072 -- 97.0
X Ray Diffraction 1.7191 1.7746 -- 142 3379 0.2379 0.2929 -- 97.0
X Ray Diffraction 1.7746 1.8381 -- 142 3381 0.2253 0.274 -- 97.0
X Ray Diffraction 1.8381 1.9117 -- 143 3367 0.2215 0.282 -- 96.0
X Ray Diffraction 1.9117 1.9987 -- 138 3357 0.2067 0.2548 -- 96.0
X Ray Diffraction 1.9987 2.104 -- 135 3328 0.1949 0.2096 -- 95.0
X Ray Diffraction 2.104 2.2359 -- 135 3269 0.1864 0.2492 -- 93.0
X Ray Diffraction 2.2359 2.4085 -- 135 3231 0.1947 0.2578 -- 92.0
X Ray Diffraction 2.4085 2.6509 -- 128 3206 0.2046 0.2644 -- 91.0
X Ray Diffraction 2.6509 3.0344 -- 136 3183 0.2142 0.2245 -- 90.0
X Ray Diffraction 3.0344 3.8228 -- 132 3118 0.1901 0.2015 -- 88.0
X Ray Diffraction 3.8228 48.3312 -- 130 3090 0.1975 0.2102 -- 86.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.6937
Anisotropic B[1][1] -1.4636
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.0938
Anisotropic B[2][2] 1.0687
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.395
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.37
f_plane_restr 0.006
f_chiral_restr 0.086
f_angle_d 1.355
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2728
Nucleic Acid Atoms 0
Heterogen Atoms 81
Solvent Atoms 265

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