X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 298.0
Details 15% PEG200, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.15 α = 90
b = 333.18 β = 90
c = 58.49 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2009-02-27
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.975500 ESRF ID14-4

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
2.28 48.06 97.0 0.053 -- -- -- 78294 75918 -3.0 -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)
2.28 2.34 98.9 0.435 -- 3.17 -- --

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 2.28 48.058 -- 2.0 78294 75914 3828 96.03 -- 0.1753 0.173 0.2194 --
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 2.28 2.361 -- 348 6568 0.2517 0.2972 -- 89.0
X Ray Diffraction 2.361 2.4556 -- 389 7282 0.2408 0.3131 -- 99.0
X Ray Diffraction 2.4556 2.5673 -- 389 7293 0.2343 0.311 -- 98.0
X Ray Diffraction 2.5673 2.7027 -- 392 7279 0.1886 0.2585 -- 98.0
X Ray Diffraction 2.7027 2.872 -- 375 7281 0.1616 0.2103 -- 98.0
X Ray Diffraction 2.872 3.0937 -- 382 7326 0.1578 0.2065 -- 98.0
X Ray Diffraction 3.0937 3.4049 -- 374 7248 0.172 0.2202 -- 97.0
X Ray Diffraction 3.4049 3.8974 -- 395 7217 0.1608 0.2041 -- 96.0
X Ray Diffraction 3.8974 4.9096 -- 397 7166 0.1299 0.1765 -- 94.0
X Ray Diffraction 4.9096 48.0689 -- 387 7426 0.1867 0.2117 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -4.2371
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.8497
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 9.0868
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.066
f_dihedral_angle_d 14.909
f_angle_d 1.018
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6663
Nucleic Acid Atoms 0
Heterogen Atoms 104
Solvent Atoms 715

Software

Computing
Computing Package Purpose
XDS Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
AMoRE Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
AMORE molecular replacement
Xscale data reduction