X-RAY DIFFRACTION Experimental Data & Validation


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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 = 48.32 α = 90
b = 75.55 β = 93.21
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 -- 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
1.72 48.24 98.2 0.064 -- -- -- -- 39518 -- -3.0 21.122
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)
1.72 1.81 99.2 0.358 -- 3.01 -- --

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 1.72 48.244 -- 1.99 -- 39514 1570 98.15 -- 0.1692 0.1679 0.2005 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 1.72 1.7756 -- 145 3482 0.2357 0.2862 -- 99.0
X Ray Diffraction 1.7756 1.839 -- 145 3462 0.2041 0.2293 -- 99.0
X Ray Diffraction 1.839 1.9127 -- 144 3474 0.1804 0.2354 -- 99.0
X Ray Diffraction 1.9127 1.9997 -- 141 3481 0.169 0.2155 -- 99.0
X Ray Diffraction 1.9997 2.1051 -- 145 3469 0.1527 0.184 -- 99.0
X Ray Diffraction 2.1051 2.237 -- 142 3464 0.1472 0.1948 -- 99.0
X Ray Diffraction 2.237 2.4097 -- 143 3453 0.1516 0.186 -- 98.0
X Ray Diffraction 2.4097 2.6522 -- 144 3439 0.1552 0.2089 -- 98.0
X Ray Diffraction 2.6522 3.036 -- 145 3437 0.1678 0.1959 -- 97.0
X Ray Diffraction 3.036 3.8247 -- 140 3377 0.1629 0.1772 -- 96.0
X Ray Diffraction 3.8247 48.2629 -- 136 3406 0.1738 0.1945 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.4172
Anisotropic B[1][1] -0.917
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.2029
Anisotropic B[2][2] -0.0099
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.9269
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.746
f_plane_restr 0.005
f_chiral_restr 0.076
f_angle_d 1.146
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2745
Nucleic Acid Atoms 0
Heterogen Atoms 87
Solvent Atoms 325

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