X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 293.0
Details 100mM Bis-tris pH 6.1-6.7, 200mM LiSO4, 16-20% PEG 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.56 α = 90
b = 180.51 β = 90
c = 78.55 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
IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2011-02-11
Diffraction Radiation
Monochromator Protocol
VariMax HF SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 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
2.34 20 96.6 0.071 -- -- -- 36510 35262 2.0 -3.0 37.35
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)
2.34 2.48 88.2 0.352 -- 2.38 -- --

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 2.343 19.638 -- 1.99 36510 35239 1764 96.79 -- 0.1741 0.1713 0.2265 --
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 2.3428 2.4061 -- 113 2145 0.2265 0.312 -- 82.0
X Ray Diffraction 2.4061 2.4767 -- 130 2462 0.2173 0.2727 -- 94.0
X Ray Diffraction 2.4767 2.5565 -- 132 2513 0.2043 0.2469 -- 96.0
X Ray Diffraction 2.5565 2.6477 -- 135 2563 0.1999 0.266 -- 98.0
X Ray Diffraction 2.6477 2.7534 -- 139 2621 0.1897 0.2616 -- 99.0
X Ray Diffraction 2.7534 2.8784 -- 137 2611 0.1963 0.2525 -- 100.0
X Ray Diffraction 2.8784 3.0296 -- 140 2654 0.1968 0.2364 -- 100.0
X Ray Diffraction 3.0296 3.2186 -- 137 2606 0.1885 0.2583 -- 100.0
X Ray Diffraction 3.2186 3.4659 -- 140 2649 0.1671 0.221 -- 100.0
X Ray Diffraction 3.4659 3.8124 -- 139 2646 0.1562 0.229 -- 99.0
X Ray Diffraction 3.8124 4.3588 -- 139 2641 0.1439 0.175 -- 98.0
X Ray Diffraction 4.3588 5.4719 -- 141 2676 0.1337 0.1935 -- 98.0
X Ray Diffraction 5.4719 19.6387 -- 142 2688 0.1685 0.2061 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.7556
Anisotropic B[1][1] 7.6486
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.9689
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.6515
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.056
f_dihedral_angle_d 11.457
f_angle_d 0.784
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5305
Nucleic Acid Atoms 0
Heterogen Atoms 59
Solvent Atoms 324

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
DM density modification
Phaser molecular replacement
Xscale data reduction
D*trek data collection