X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 289.0
Details 0.17 M sodium acetate, 0.085 M Tris, 25.5% PEG 4000, and 15% glycerol and directly frozen , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.37 α = 89.92
b = 60.4 β = 89.96
c = 194.03 γ = 79.75
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NOIR-1 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.00 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
2.72 45.06 97.8 0.097 -- -- 1.92 -- 70840 1.5 2.0 --
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)
2.72 2.82 97.5 0.422 -- 1.6 1.92 7013

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 2.72 43.762 -- 1.96 -- 70695 3555 97.62 -- 0.2015 0.199 0.2469 --
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 2.72 2.7573 -- 131 2673 0.3092 0.4028 -- 97.0
X Ray Diffraction 2.7573 2.7966 -- 149 2612 0.2875 0.3399 -- 97.0
X Ray Diffraction 2.7966 2.8384 -- 146 2675 0.2942 0.366 -- 98.0
X Ray Diffraction 2.8384 2.8827 -- 137 2767 0.2981 0.3701 -- 98.0
X Ray Diffraction 2.8827 2.93 -- 147 2580 0.2906 0.3591 -- 97.0
X Ray Diffraction 2.93 2.9805 -- 150 2754 0.2748 0.3354 -- 97.0
X Ray Diffraction 2.9805 3.0347 -- 141 2673 0.2729 0.3684 -- 98.0
X Ray Diffraction 3.0347 3.093 -- 146 2655 0.267 0.3362 -- 98.0
X Ray Diffraction 3.093 3.1561 -- 143 2726 0.2525 0.3193 -- 98.0
X Ray Diffraction 3.1561 3.2247 -- 151 2685 0.2418 0.3067 -- 97.0
X Ray Diffraction 3.2247 3.2997 -- 149 2682 0.259 0.3077 -- 98.0
X Ray Diffraction 3.2997 3.3822 -- 132 2708 0.2485 0.3271 -- 98.0
X Ray Diffraction 3.3822 3.4736 -- 152 2638 0.213 0.3054 -- 98.0
X Ray Diffraction 3.4736 3.5758 -- 140 2783 0.2018 0.2488 -- 98.0
X Ray Diffraction 3.5758 3.6912 -- 159 2655 0.1911 0.2398 -- 98.0
X Ray Diffraction 3.6912 3.823 -- 140 2659 0.1733 0.2164 -- 98.0
X Ray Diffraction 3.823 3.976 -- 129 2686 0.1668 0.2427 -- 97.0
X Ray Diffraction 3.976 4.1568 -- 128 2699 0.146 0.1932 -- 98.0
X Ray Diffraction 4.1568 4.3758 -- 147 2711 0.151 0.1552 -- 98.0
X Ray Diffraction 4.3758 4.6496 -- 148 2783 0.1326 0.1771 -- 98.0
X Ray Diffraction 4.6496 5.0082 -- 130 2686 0.1553 0.1844 -- 98.0
X Ray Diffraction 5.0082 5.5113 -- 149 2706 0.1645 0.2078 -- 98.0
X Ray Diffraction 5.5113 6.3068 -- 136 2648 0.1805 0.2313 -- 98.0
X Ray Diffraction 6.3068 7.9381 -- 150 2681 0.1811 0.1913 -- 98.0
X Ray Diffraction 7.9381 43.7673 -- 125 2615 0.1825 0.1827 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.9641
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.75
f_plane_restr 0.007
f_chiral_restr 0.048
f_angle_d 1.166
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14772
Nucleic Acid Atoms 2948
Heterogen Atoms 192
Solvent Atoms 372

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
DTREK Data Reduction (intensity integration)
DTREK Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
D*trek version: 9.9.8.0L data reduction
D*trek data collection