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 = 48.59 α = 90
b = 75.37 β = 93.25
c = 52.63 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
1.52 48.51 93.4 0.043 -- -- -- -- 54399 -- -3.0 20.267
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)
1.52 1.6 97.2 0.335 -- 3.0 -- --

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 1.52 48.512 -- 2.0 -- 54399 2170 93.4 -- 0.1704 0.1695 0.1903 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 1.52 1.5554 -- 153 3586 0.2246 0.2498 -- 97.0
X Ray Diffraction 1.5554 1.5943 -- 149 3618 0.2011 0.2252 -- 98.0
X Ray Diffraction 1.5943 1.6374 -- 155 3577 0.192 0.2272 -- 97.0
X Ray Diffraction 1.6374 1.6856 -- 141 3590 0.186 0.2348 -- 96.0
X Ray Diffraction 1.6856 1.74 -- 154 3565 0.1719 0.204 -- 96.0
X Ray Diffraction 1.74 1.8022 -- 145 3583 0.1727 0.2124 -- 96.0
X Ray Diffraction 1.8022 1.8743 -- 146 3515 0.167 0.2136 -- 95.0
X Ray Diffraction 1.8743 1.9596 -- 144 3511 0.1727 0.2232 -- 95.0
X Ray Diffraction 1.9596 2.0629 -- 146 3485 0.1615 0.1964 -- 94.0
X Ray Diffraction 2.0629 2.1922 -- 141 3513 0.158 0.1909 -- 93.0
X Ray Diffraction 2.1922 2.3614 -- 140 3421 0.1648 0.179 -- 92.0
X Ray Diffraction 2.3614 2.5991 -- 140 3372 0.1653 0.2029 -- 90.0
X Ray Diffraction 2.5991 2.9751 -- 138 3344 0.1745 0.1866 -- 90.0
X Ray Diffraction 2.9751 3.7481 -- 144 3299 0.1656 0.17 -- 88.0
X Ray Diffraction 3.7481 48.5365 -- 134 3250 0.1573 0.1481 -- 85.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.1411
Anisotropic B[1][1] -0.8163
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.1031
Anisotropic B[2][2] -0.0067
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.823
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.94
f_plane_restr 0.006
f_chiral_restr 0.078
f_angle_d 1.272
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2752
Nucleic Acid Atoms 0
Heterogen Atoms 86
Solvent Atoms 335

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