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 320 mM sodium chloride, 100 mM HEPES, 30% PEG3350, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.67 α = 90
b = 81.55 β = 110.32
c = 58.72 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
PIXEL DECTRIS PILATUS 6M -- 2011-10-22
Diffraction Radiation
Monochromator Protocol
liquid nitrogen cooled channel-cut Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.97934 ESRF ID29

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 45.64 99.2 -- 0.087 -- 3.4 -- 41002 0.0 0.0 --
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)
1.85 1.96 98.2 -- 0.458 2.22 3.4 6430

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 45.636 -- 2.01 -- 40985 2049 99.31 -- 0.2096 0.2075 0.2499 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 1.85 1.8932 -- 134 2531 0.2826 0.3242 -- 97.0
X Ray Diffraction 1.8932 1.9406 -- 135 2573 0.2645 0.2868 -- 100.0
X Ray Diffraction 1.9406 1.9931 -- 135 2565 0.2465 0.3286 -- 99.0
X Ray Diffraction 1.9931 2.0517 -- 137 2596 0.2321 0.2645 -- 100.0
X Ray Diffraction 2.0517 2.1179 -- 137 2594 0.2162 0.2381 -- 100.0
X Ray Diffraction 2.1179 2.1936 -- 137 2599 0.2109 0.2716 -- 100.0
X Ray Diffraction 2.1936 2.2814 -- 137 2607 0.2181 0.2652 -- 100.0
X Ray Diffraction 2.2814 2.3853 -- 137 2596 0.2243 0.2936 -- 100.0
X Ray Diffraction 2.3853 2.511 -- 136 2602 0.2194 0.3051 -- 100.0
X Ray Diffraction 2.511 2.6683 -- 137 2600 0.2208 0.2603 -- 100.0
X Ray Diffraction 2.6683 2.8743 -- 137 2597 0.2239 0.2838 -- 100.0
X Ray Diffraction 2.8743 3.1635 -- 137 2601 0.2121 0.2457 -- 99.0
X Ray Diffraction 3.1635 3.6211 -- 138 2615 0.1958 0.1887 -- 100.0
X Ray Diffraction 3.6211 4.5616 -- 138 2624 0.1799 0.2358 -- 99.0
X Ray Diffraction 4.5616 45.6496 -- 137 2636 0.2028 0.2465 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 3.4824
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 7.6433
Anisotropic B[2][2] 4.5723
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.0547
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.004
f_dihedral_angle_d 16.007
f_chiral_restr 0.051
f_plane_restr 0.003
f_angle_d 0.764
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3777
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 179

Software

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