X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 293.0
Details 5% (w/v) PEG 4000, 10mM Tris-HCl, 300mM NaCl , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117.27 α = 90
b = 120.39 β = 112.46
c = 58.72 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 96
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2010-02-10
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C

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 50 73.2 -- -- -- -- 25104 25104 0.0 0.0 --

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 2.42 35.689 -- 1.35 23792 23775 1186 82.64 -- 0.1941 0.1909 0.2534 --
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 2.4201 2.5302 -- 82 1588 0.179 0.2442 -- 46.0
X Ray Diffraction 2.5302 2.6635 -- 93 2025 0.2248 0.2883 -- 59.0
X Ray Diffraction 2.6635 2.8303 -- 110 2471 0.2526 0.296 -- 73.0
X Ray Diffraction 2.8303 3.0488 -- 154 3048 0.2624 0.3828 -- 89.0
X Ray Diffraction 3.0488 3.3554 -- 187 3337 0.2184 0.3125 -- 98.0
X Ray Diffraction 3.3554 3.8404 -- 179 3383 0.1776 0.242 -- 99.0
X Ray Diffraction 3.8404 4.8366 -- 176 3359 0.1461 0.2106 -- 99.0
X Ray Diffraction 4.8366 35.6933 -- 205 3378 0.1724 0.2034 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.8829
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.6509
Anisotropic B[2][2] -3.5115
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.3945
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.086
f_dihedral_angle_d 21.974
f_angle_d 1.578
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2530
Nucleic Acid Atoms 590
Heterogen Atoms 41
Solvent Atoms 256

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_1145) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHASER model building
ADSC version: Quantum data collection