X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 10% v/v MPD, 40 mM NaCacodylate pH 7.0, 12 mM Spermine tetra-HCl, 80 mM Sodium Chloride, 12mM Potassium Chloride, 20 mM Magnesium Chloride , VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.44 α = 90
b = 46.44 β = 90
c = 120.61 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-07-29
Diffraction Radiation
Monochromator Protocol
Double crystal, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.2 0.9795 ALS 8.2.2

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
1.5 40.22 97.33 -- 0.08 -- 4.1 24918 24253 -- -- --
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)
1.5 1.55 64.6 -- 0.35 2.4 2.1 --

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
246D 1.5 40.22 -- 2.0 23662 22895 1228 96.76 0.2248 0.20975 0.20826 0.23807 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 1.501 1.54 -- 64 1186 0.311 0.282 -- 73.62
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.552
Anisotropic B[1][1] 0.93
Anisotropic B[1][2] 0.46
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.93
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.39
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.025
r_chiral_restr 0.115
r_angle_refined_deg 2.305
r_bond_refined_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 1002
Heterogen Atoms 2
Solvent Atoms 143

Software

Computing
Computing Package Purpose
Web-ICE Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Phaser Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
Phaser model building
Web-ICE data collection