X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.15
Details 50mM MES, 2% PEG8000, 30% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.77 α = 90
b = 85.97 β = 90
c = 88.73 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2010-11-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4

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
1.65 30 99.9 -- -- -- -- -- 79417 0.0 0.0 18.42
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)
1.65 1.74 99.5 -- -- -- -- --

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 1.65 29.576 -- 1.33 -- 75264 3988 99.78 -- 0.1749 0.1733 0.2055 5
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 1.65 1.6701 -- 130 2633 0.2824 0.3276 -- 98.0
X Ray Diffraction 1.6701 1.6913 -- 124 2673 0.2648 0.2679 -- 99.0
X Ray Diffraction 1.6913 1.7135 -- 149 2651 0.2495 0.2804 -- 100.0
X Ray Diffraction 1.7135 1.737 -- 161 2616 0.2428 0.3003 -- 100.0
X Ray Diffraction 1.737 1.7618 -- 143 2703 0.2283 0.2769 -- 100.0
X Ray Diffraction 1.7618 1.7881 -- 142 2644 0.2189 0.2383 -- 100.0
X Ray Diffraction 1.7881 1.816 -- 149 2656 0.2111 0.2386 -- 100.0
X Ray Diffraction 1.816 1.8458 -- 138 2650 0.2063 0.2551 -- 100.0
X Ray Diffraction 1.8458 1.8776 -- 123 2695 0.1871 0.2485 -- 100.0
X Ray Diffraction 1.8776 1.9118 -- 141 2663 0.1862 0.2231 -- 100.0
X Ray Diffraction 1.9118 1.9485 -- 136 2674 0.1782 0.2243 -- 100.0
X Ray Diffraction 1.9485 1.9883 -- 145 2684 0.1951 0.2148 -- 100.0
X Ray Diffraction 1.9883 2.0315 -- 153 2665 0.1801 0.2414 -- 100.0
X Ray Diffraction 2.0315 2.0788 -- 151 2641 0.1803 0.2078 -- 100.0
X Ray Diffraction 2.0788 2.1307 -- 145 2702 0.1806 0.2231 -- 100.0
X Ray Diffraction 2.1307 2.1883 -- 141 2659 0.1804 0.2022 -- 100.0
X Ray Diffraction 2.1883 2.2527 -- 148 2699 0.1681 0.2241 -- 100.0
X Ray Diffraction 2.2527 2.3254 -- 143 2674 0.171 0.2072 -- 100.0
X Ray Diffraction 2.3254 2.4084 -- 150 2668 0.1674 0.2106 -- 100.0
X Ray Diffraction 2.4084 2.5048 -- 149 2695 0.1646 0.1823 -- 100.0
X Ray Diffraction 2.5048 2.6188 -- 149 2702 0.1621 0.2072 -- 100.0
X Ray Diffraction 2.6188 2.7567 -- 124 2723 0.1537 0.1836 -- 100.0
X Ray Diffraction 2.7567 2.9293 -- 138 2700 0.1552 0.17 -- 100.0
X Ray Diffraction 2.9293 3.1552 -- 152 2719 0.1623 0.2027 -- 100.0
X Ray Diffraction 3.1552 3.4723 -- 155 2705 0.1607 0.2214 -- 100.0
X Ray Diffraction 3.4723 3.9738 -- 141 2745 0.1491 0.1527 -- 100.0
X Ray Diffraction 3.9738 5.0026 -- 136 2781 0.1357 0.1696 -- 99.0
X Ray Diffraction 5.0026 29.5804 -- 132 2912 0.2015 0.2091 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.5965
Anisotropic B[1][1] -1.669
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.7365
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.0675
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.103
f_plane_restr 0.013
f_chiral_restr 0.148
f_angle_d 1.894
f_bond_d 0.021
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5000
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 450

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
MOLREP model building
DNA data collection