X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7
Temperature 298.0
Details PEG3350, NH4SO4, JM600, pH 7, vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 159.59 α = 90
b = 159.59 β = 90
c = 689.65 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR ADSC QUANTUM 315r -- 2011-01-01
Diffraction Radiation
Monochromator Protocol
Cryogenically-cooled double crystal Si(111) monochromator. Triple striped vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9798 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
3.68 114.94 99.9 -- -- -- 3.9 37324 37324 2.0 2.0 --
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)
3.68 3.78 100.0 0.625 0.625 1.1 4.0 2715

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 3.68 97.6654 -- 0.0 33612 33612 1703 89.93 0.2457 0.2457 0.2443 0.2719 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 3.68 3.7883 -- 130 2296 0.3524 0.3818 -- 79.0
X Ray Diffraction 3.7883 3.9106 -- 115 2350 0.3179 0.3274 -- 80.0
X Ray Diffraction 3.9106 4.0504 -- 131 2457 0.2877 0.2744 -- 85.0
X Ray Diffraction 4.0504 4.2125 -- 156 2546 0.2599 0.296 -- 87.0
X Ray Diffraction 4.2125 4.4043 -- 153 2598 0.2325 0.2588 -- 89.0
X Ray Diffraction 4.4043 4.6365 -- 138 2710 0.2069 0.217 -- 92.0
X Ray Diffraction 4.6365 4.9269 -- 146 2756 0.197 0.2671 -- 94.0
X Ray Diffraction 4.9269 5.3073 -- 137 2760 0.2242 0.2685 -- 93.0
X Ray Diffraction 5.3073 5.8414 -- 136 2740 0.2402 0.3009 -- 93.0
X Ray Diffraction 5.8414 6.6865 -- 154 2784 0.2415 0.3234 -- 93.0
X Ray Diffraction 6.6865 8.4235 -- 162 2813 0.2135 0.2385 -- 94.0
X Ray Diffraction 8.4235 97.6654 -- 145 3099 0.2477 0.2277 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 95.6005
Anisotropic B[1][1] 4.2364
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.2364
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.4729
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.955
f_plane_restr 0.003
f_chiral_restr 0.041
f_angle_d 0.635
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12881
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 5

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
DENZO Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
phaser Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
SCALA version: 3.3.9 data reduction