X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 277.0
Details 0.05 M sodium cacodylate, 32% 2-methyl-2,4-pentanediol (MPD), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 103.68 α = 90
b = 103.68 β = 90
c = 556.38 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2012-08-15
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 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
3.09 139.09 97.4 0.039 0.039 -- 2.9 61627 60025 -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)
3.09 3.26 97.9 0.487 0.487 1.5 2.9 --

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 3.09 85.45 -- 1.35 61484 59664 3025 97.04 -- 0.2325 0.2313 0.2548 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 3.09 3.1391 -- 155 2448 0.356 0.3427 -- 92.0
X Ray Diffraction 3.1391 3.1906 -- 123 2591 0.3425 0.3251 -- 99.0
X Ray Diffraction 3.1906 3.2456 -- 153 2637 0.3382 0.3846 -- 99.0
X Ray Diffraction 3.2456 3.3046 -- 156 2545 0.3217 0.3957 -- 98.0
X Ray Diffraction 3.3046 3.3682 -- 138 2577 0.3071 0.357 -- 97.0
X Ray Diffraction 3.3682 3.437 -- 130 2575 0.2988 0.2857 -- 97.0
X Ray Diffraction 3.437 3.5117 -- 145 2512 0.2834 0.293 -- 97.0
X Ray Diffraction 3.5117 3.5934 -- 131 2694 0.262 0.3181 -- 100.0
X Ray Diffraction 3.5934 3.6832 -- 120 2648 0.2568 0.293 -- 100.0
X Ray Diffraction 3.6832 3.7828 -- 137 2614 0.2665 0.3051 -- 99.0
X Ray Diffraction 3.7828 3.8941 -- 138 2655 0.2621 0.3134 -- 100.0
X Ray Diffraction 3.8941 4.0198 -- 145 2633 0.2539 0.2937 -- 99.0
X Ray Diffraction 4.0198 4.1635 -- 128 2637 0.2446 0.2655 -- 98.0
X Ray Diffraction 4.1635 4.3302 -- 113 2575 0.2398 0.29 -- 97.0
X Ray Diffraction 4.3302 4.5273 -- 142 2509 0.2357 0.2671 -- 94.0
X Ray Diffraction 4.5273 4.7659 -- 137 2538 0.2227 0.2603 -- 97.0
X Ray Diffraction 4.7659 5.0645 -- 153 2616 0.219 0.2299 -- 99.0
X Ray Diffraction 5.0645 5.4555 -- 152 2658 0.232 0.2402 -- 99.0
X Ray Diffraction 5.4555 6.0044 -- 138 2556 0.2407 0.2711 -- 97.0
X Ray Diffraction 6.0044 6.8729 -- 141 2423 0.2468 0.2839 -- 91.0
X Ray Diffraction 6.8729 8.6578 -- 132 2583 0.1926 0.185 -- 97.0
X Ray Diffraction 8.6578 85.483 -- 118 2415 0.161 0.1693 -- 90.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 78.24
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_chiral_restr 0.033
f_dihedral_angle_d 21.316
f_angle_d 0.611
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9635
Nucleic Acid Atoms 5986
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Phaser (CCP4-6.1.1) Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
Phaser version: (CCP4-6.1.1) model building
ADSC version: Quantum data collection