X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details 2 microliter protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliter reservoir buffer(100 mM HEPES, 30 % (w/v) polyethylene glycol (PEG) 6000, pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.16 α = 90
b = 69.21 β = 90.11
c = 83.85 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 -- Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror 2005-06-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.5418 ALS 4.2.2

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
2.5 53.38 99.2 -- 0.107 -- 3.58 -- 27431 -- -- --
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)
2.5 2.59 96.7 -- -- 3.5 3.38 --

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 2.5 53.378 -- 1.36 -- 27431 3712 94.7 -- 0.1813 0.1762 0.2466 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 2.5 2.5316 -- 127 1546 0.2725 0.3552 -- 81.0
X Ray Diffraction 2.5316 2.565 -- 132 1708 0.2431 0.3054 -- 91.0
X Ray Diffraction 2.565 2.6001 -- 132 1653 0.2391 0.3465 -- 93.0
X Ray Diffraction 2.6001 2.6372 -- 125 1763 0.2276 0.2708 -- 93.0
X Ray Diffraction 2.6372 2.6766 -- 144 1660 0.2164 0.3583 -- 92.0
X Ray Diffraction 2.6766 2.7184 -- 130 1705 0.2126 0.2627 -- 91.0
X Ray Diffraction 2.7184 2.763 -- 137 1725 0.2139 0.3049 -- 93.0
X Ray Diffraction 2.763 2.8106 -- 143 1729 0.2217 0.3401 -- 94.0
X Ray Diffraction 2.8106 2.8617 -- 140 1799 0.2109 0.2921 -- 94.0
X Ray Diffraction 2.8617 2.9168 -- 127 1666 0.2108 0.3033 -- 94.0
X Ray Diffraction 2.9168 2.9763 -- 133 1780 0.1948 0.2604 -- 95.0
X Ray Diffraction 2.9763 3.041 -- 147 1745 0.2172 0.2842 -- 95.0
X Ray Diffraction 3.041 3.1117 -- 129 1721 0.1946 0.2999 -- 95.0
X Ray Diffraction 3.1117 3.1896 -- 146 1762 0.1914 0.3199 -- 95.0
X Ray Diffraction 3.1896 3.2758 -- 142 1749 0.1789 0.2517 -- 95.0
X Ray Diffraction 3.2758 3.3722 -- 149 1804 0.1784 0.2604 -- 96.0
X Ray Diffraction 3.3722 3.481 -- 136 1738 0.178 0.238 -- 96.0
X Ray Diffraction 3.481 3.6054 -- 136 1802 0.1688 0.2471 -- 95.0
X Ray Diffraction 3.6054 3.7497 -- 142 1718 0.1693 0.2025 -- 94.0
X Ray Diffraction 3.7497 3.9203 -- 129 1783 0.1683 0.2477 -- 97.0
X Ray Diffraction 3.9203 4.1269 -- 143 1790 0.1677 0.278 -- 97.0
X Ray Diffraction 4.1269 4.3854 -- 145 1824 0.131 0.1907 -- 98.0
X Ray Diffraction 4.3854 4.7238 -- 149 1774 0.1336 0.1705 -- 98.0
X Ray Diffraction 4.7238 5.1988 -- 132 1882 0.1327 0.1997 -- 99.0
X Ray Diffraction 5.1988 5.9502 -- 138 1794 0.1461 0.2287 -- 99.0
X Ray Diffraction 5.9502 7.4933 -- 135 1844 0.1689 0.2239 -- 99.0
X Ray Diffraction 7.4933 53.3899 -- 144 1834 0.1408 0.1494 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.19
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.157
f_chiral_restr 0.047
f_dihedral_angle_d 11.906
f_bond_d 0.009
f_plane_restr 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6096
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 252

Software

Software
Software Name Purpose
PHENIX refinement version: (phenix.refine: 1.8.2_1309)
CNS refinement
Blu-Ice data collection
d*TREK data reduction
d*TREK data scaling
CNS phasing