X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

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

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.1 α = 90
b = 180.31 β = 90
c = 79.43 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 Compound Refractive Lenses 2011-09-25
Diffraction Radiation
Monochromator Protocol
DCM SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 0.96110 DIAMOND I04

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
2.44 79.43 99.6 -- 0.091 -- 3.8 32370 32370 1.7 1.7 --
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)
2.44 2.5 99.8 0.674 0.674 1.1 3.7 --

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 2.44 59.598 -- 1.34 32370 32318 1639 99.53 -- 0.1895 0.1873 0.2301 --
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 2.44 2.5118 -- 140 2504 0.2823 0.3126 -- 100.0
X Ray Diffraction 2.5118 2.5929 -- 153 2525 0.2542 0.3345 -- 100.0
X Ray Diffraction 2.5929 2.6856 -- 131 2530 0.2403 0.2682 -- 100.0
X Ray Diffraction 2.6856 2.7931 -- 119 2523 0.2291 0.2845 -- 100.0
X Ray Diffraction 2.7931 2.9202 -- 140 2537 0.2259 0.2862 -- 100.0
X Ray Diffraction 2.9202 3.0742 -- 171 2504 0.205 0.2576 -- 100.0
X Ray Diffraction 3.0742 3.2668 -- 137 2533 0.2098 0.2358 -- 100.0
X Ray Diffraction 3.2668 3.519 -- 133 2547 0.1854 0.2131 -- 100.0
X Ray Diffraction 3.519 3.873 -- 127 2533 0.1629 0.2185 -- 98.0
X Ray Diffraction 3.873 4.4333 -- 136 2550 0.1565 0.2115 -- 98.0
X Ray Diffraction 4.4333 5.5849 -- 127 2614 0.1522 0.1867 -- 100.0
X Ray Diffraction 5.5849 59.6162 -- 125 2779 0.1773 0.1946 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.3534
Anisotropic B[1][1] -8.2041
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 9.9362
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.7256
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_chiral_restr 0.044
f_dihedral_angle_d 10.855
f_angle_d 0.574
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5376
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 152

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
SCALA 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
Phaser molecular replacement
SCALA version: 3.3.16 data reduction