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 triphosphate, 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 = 53.03 α = 90
b = 72.75 β = 90
c = 119.46 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 -- 2013-07-24
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
1.73 53 100.0 -- -- -- -- 49311 49311 -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)
1.727 1.76 99.2 -- -- -- -- --

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 1.727 48.465 -- 1.33 49282 49036 3896 99.53 -- 0.1658 0.1632 0.196 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 1.7273 1.7483 -- 138 1532 0.2233 0.2766 -- 97.0
X Ray Diffraction 1.7483 1.7705 -- 157 1561 0.1941 0.2592 -- 98.0
X Ray Diffraction 1.7705 1.7938 -- 133 1572 0.1813 0.1957 -- 99.0
X Ray Diffraction 1.7938 1.8183 -- 137 1577 0.1671 0.2187 -- 99.0
X Ray Diffraction 1.8183 1.8443 -- 140 1593 0.1643 0.2199 -- 99.0
X Ray Diffraction 1.8443 1.8719 -- 136 1575 0.1534 0.2068 -- 99.0
X Ray Diffraction 1.8719 1.9011 -- 123 1598 0.1488 0.1802 -- 100.0
X Ray Diffraction 1.9011 1.9323 -- 119 1591 0.1518 0.1975 -- 99.0
X Ray Diffraction 1.9323 1.9656 -- 143 1635 0.1475 0.1938 -- 99.0
X Ray Diffraction 1.9656 2.0013 -- 124 1585 0.1587 0.2129 -- 100.0
X Ray Diffraction 2.0013 2.0398 -- 150 1602 0.1569 0.1948 -- 99.0
X Ray Diffraction 2.0398 2.0815 -- 136 1586 0.1586 0.1897 -- 100.0
X Ray Diffraction 2.0815 2.1267 -- 150 1587 0.157 0.1999 -- 100.0
X Ray Diffraction 2.1267 2.1762 -- 144 1578 0.1587 0.2235 -- 100.0
X Ray Diffraction 2.1762 2.2306 -- 141 1599 0.1517 0.1664 -- 100.0
X Ray Diffraction 2.2306 2.2909 -- 150 1611 0.1562 0.217 -- 100.0
X Ray Diffraction 2.2909 2.3583 -- 124 1606 0.157 0.2177 -- 100.0
X Ray Diffraction 2.3583 2.4345 -- 122 1655 0.1615 0.208 -- 100.0
X Ray Diffraction 2.4345 2.5215 -- 156 1593 0.1633 0.1964 -- 100.0
X Ray Diffraction 2.5215 2.6224 -- 136 1620 0.1816 0.2116 -- 100.0
X Ray Diffraction 2.6224 2.7418 -- 136 1620 0.1712 0.209 -- 100.0
X Ray Diffraction 2.7418 2.8863 -- 155 1609 0.1728 0.1965 -- 100.0
X Ray Diffraction 2.8863 3.0671 -- 131 1645 0.1707 0.1882 -- 100.0
X Ray Diffraction 3.0671 3.3039 -- 136 1660 0.1683 0.2129 -- 100.0
X Ray Diffraction 3.3039 3.6362 -- 143 1634 0.165 0.1915 -- 100.0
X Ray Diffraction 3.6362 4.1622 -- 139 1666 0.1445 0.1648 -- 100.0
X Ray Diffraction 4.1622 5.2429 -- 145 1674 0.1422 0.1574 -- 100.0
X Ray Diffraction 5.2429 48.4842 -- 152 1776 0.1932 0.1998 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.07
f_dihedral_angle_d 20.11
f_angle_d 1.126
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2738
Nucleic Acid Atoms 169
Heterogen Atoms 79
Solvent Atoms 395

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