X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 298.0
Details 100 mM sodium citrate, pH 5.0, 2 mM guanosine diphosphate, 100mM magnesium chloride,18-24% PEG 6000,1.1 mM short DNA strand , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.44 α = 90
b = 73.12 β = 90
c = 119.04 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 130
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2013-08-14
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25

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
1.8 46.2 97.8 -- -- -- -- 44706 43723 -999.0 -3.0 --
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)
1.8 1.9 97.6 -- -- -- -- --

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 refinement 1.8 40.995 -- 1.34 44862 43651 3439 97.33 -- 0.1675 0.1644 0.2056 8% of data chosen at 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 1.8 1.8247 -- 123 1642 0.2228 0.2708 -- 98.0
X Ray Diffraction 1.8247 1.8507 -- 144 1562 0.2063 0.2732 -- 98.0
X Ray Diffraction 1.8507 1.8784 -- 146 1565 0.1925 0.2308 -- 97.0
X Ray Diffraction 1.8784 1.9077 -- 148 1539 0.1795 0.2035 -- 97.0
X Ray Diffraction 1.9077 1.939 -- 127 1620 0.1759 0.2408 -- 98.0
X Ray Diffraction 1.939 1.9724 -- 113 1616 0.1712 0.2471 -- 98.0
X Ray Diffraction 1.9724 2.0083 -- 141 1587 0.1746 0.2242 -- 98.0
X Ray Diffraction 2.0083 2.0469 -- 138 1562 0.1687 0.2305 -- 96.0
X Ray Diffraction 2.0469 2.0887 -- 140 1619 0.1586 0.1952 -- 98.0
X Ray Diffraction 2.0887 2.1341 -- 142 1564 0.1582 0.2156 -- 98.0
X Ray Diffraction 2.1341 2.1838 -- 135 1601 0.1563 0.2082 -- 97.0
X Ray Diffraction 2.1838 2.2384 -- 136 1588 0.1632 0.2155 -- 98.0
X Ray Diffraction 2.2384 2.2989 -- 140 1578 0.16 0.2374 -- 96.0
X Ray Diffraction 2.2989 2.3665 -- 139 1621 0.1625 0.2292 -- 98.0
X Ray Diffraction 2.3665 2.4429 -- 119 1607 0.1653 0.235 -- 98.0
X Ray Diffraction 2.4429 2.5302 -- 151 1600 0.1668 0.2327 -- 97.0
X Ray Diffraction 2.5302 2.6315 -- 129 1633 0.1755 0.2114 -- 99.0
X Ray Diffraction 2.6315 2.7512 -- 147 1592 0.1628 0.2185 -- 98.0
X Ray Diffraction 2.7512 2.8962 -- 149 1626 0.1668 0.1884 -- 98.0
X Ray Diffraction 2.8962 3.0776 -- 138 1618 0.1651 0.1901 -- 98.0
X Ray Diffraction 3.0776 3.3152 -- 132 1663 0.1679 0.1853 -- 99.0
X Ray Diffraction 3.3152 3.6486 -- 139 1676 0.1611 0.1945 -- 99.0
X Ray Diffraction 3.6486 4.1761 -- 139 1637 0.1466 0.1792 -- 98.0
X Ray Diffraction 4.1761 5.2597 -- 137 1637 0.1432 0.1736 -- 96.0
X Ray Diffraction 5.2597 41.006 -- 147 1659 0.1788 0.2136 -- 92.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.071
f_dihedral_angle_d 15.352
f_angle_d 1.084
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2738
Nucleic Acid Atoms 202
Heterogen Atoms 58
Solvent Atoms 440

Software

Computing
Computing Package Purpose
CBASS Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.2_1309) refinement
PHENIX model building
CBASS data collection