X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.8
Temperature 298.0
Details 1.6 M sodium citrate, 50 mM TRIS Chloride, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.19 α = 90
b = 41.01 β = 104.51
c = 71.54 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
IMAGE PLATE RIGAKU RAXIS IV++ -- 2011-04-18
Diffraction Radiation
Monochromator Protocol
Varimax optics SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
1.7 20 90.9 0.088 -- -- 6.8 -- 23826 -- -- --
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)
1.7 1.76 89.2 0.549 -- -- 7.0 --

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 1.7024 19.909 -- 1.34 26211 23826 1982 90.9 -- 0.1742 0.1717 0.2006 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 1.7024 1.7449 -- 133 1488 0.253 0.2914 -- 87.0
X Ray Diffraction 1.7449 1.7921 -- 146 1533 0.2283 0.3105 -- 90.0
X Ray Diffraction 1.7921 1.8448 -- 133 1545 0.1922 0.2379 -- 90.0
X Ray Diffraction 1.8448 1.9043 -- 148 1498 0.1712 0.2155 -- 89.0
X Ray Diffraction 1.9043 1.9723 -- 131 1531 0.1427 0.2232 -- 89.0
X Ray Diffraction 1.9723 2.0512 -- 134 1520 0.1489 0.2036 -- 88.0
X Ray Diffraction 2.0512 2.1444 -- 139 1487 0.1466 0.2061 -- 88.0
X Ray Diffraction 2.1444 2.2573 -- 135 1528 0.1574 0.2173 -- 89.0
X Ray Diffraction 2.2573 2.3986 -- 138 1553 0.1505 0.1947 -- 91.0
X Ray Diffraction 2.3986 2.5834 -- 140 1580 0.1647 0.2035 -- 92.0
X Ray Diffraction 2.5834 2.8427 -- 151 1625 0.1697 0.1869 -- 95.0
X Ray Diffraction 2.8427 3.2525 -- 151 1652 0.1717 0.2142 -- 95.0
X Ray Diffraction 3.2525 4.092 -- 149 1621 0.1582 0.1664 -- 94.0
X Ray Diffraction 4.092 19.91 -- 154 1683 0.1966 0.1946 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 2.5341
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.5539
Anisotropic B[2][2] -7.1554
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.6213
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_chiral_restr 0.078
f_dihedral_angle_d 13.726
f_angle_d 1.304
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2048
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 114

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
HKL data reduction