X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.75
Temperature 291.0
Details 300-340 mM NaCl, 100 mM Hepes, 24-32 % PEG 3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.89 α = 90
b = 84.06 β = 108.78
c = 58.36 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
CCD ADSC QUANTUM 315r -- 2012-06-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 1.07231 ESRF ID23-1

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
1.85 46.4 99.7 -- 0.06 -- 7.4 -- 43567 -- -- --
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)
1.85 1.96 99.8 0.41 -- 5.1 7.4 --

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 1.85 27.569 -- 2.01 -- 43551 2177 99.84 -- 0.1688 0.1671 0.2024 Random selection
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 1.85 1.8902 -- 134 2551 0.2108 0.2462 -- 100.0
X Ray Diffraction 1.8902 1.9342 -- 137 2584 0.1946 0.2493 -- 100.0
X Ray Diffraction 1.9342 1.9825 -- 135 2568 0.1847 0.2459 -- 100.0
X Ray Diffraction 1.9825 2.0361 -- 135 2569 0.1799 0.2419 -- 100.0
X Ray Diffraction 2.0361 2.096 -- 136 2596 0.1788 0.2242 -- 100.0
X Ray Diffraction 2.096 2.1636 -- 135 2582 0.1727 0.233 -- 100.0
X Ray Diffraction 2.1636 2.2409 -- 137 2603 0.1699 0.209 -- 100.0
X Ray Diffraction 2.2409 2.3306 -- 137 2590 0.1704 0.208 -- 100.0
X Ray Diffraction 2.3306 2.4366 -- 136 2579 0.1673 0.1974 -- 100.0
X Ray Diffraction 2.4366 2.565 -- 134 2561 0.1632 0.2263 -- 100.0
X Ray Diffraction 2.565 2.7256 -- 137 2586 0.1672 0.18 -- 100.0
X Ray Diffraction 2.7256 2.9358 -- 136 2593 0.1662 0.2107 -- 100.0
X Ray Diffraction 2.9358 3.2308 -- 137 2609 0.1672 0.2107 -- 100.0
X Ray Diffraction 3.2308 3.6974 -- 137 2599 0.1563 0.1834 -- 100.0
X Ray Diffraction 3.6974 4.6547 -- 137 2608 0.1415 0.1663 -- 100.0
X Ray Diffraction 4.6547 27.572 -- 137 2596 0.1841 0.2058 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.979
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 4.2975
Anisotropic B[2][2] 1.2003
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.7788
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_angle_d 0.966
f_bond_d 0.006
f_chiral_restr 0.064
f_dihedral_angle_d 18.342
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3820
Nucleic Acid Atoms 0
Heterogen Atoms 78
Solvent Atoms 273

Software

Software
Software Name Purpose
PHENIX refinement version: (phenix.refine: 1.6.4_486)
PHENIX phasing version: (phenix.refine: 1.6.4_486)
XSCALE data scaling
XDS data reduction