X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 291.0
Details 0.1M Sodium Cacodylate, 0.2M Calcium Acetate, 11.5% Peg8000, 3% 1,5 diaminopentane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 180.5 α = 90
b = 113.3 β = 90
c = 126.6 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 108
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR ADSC QUANTUM 315 -- 2012-04-16
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E

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
2.9 50 95.2 0.113 -- -- 3.4 57810 55035 -- 0.0 --
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)
2.9 3.0 89.4 0.397 -- -- 2.4 5094

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 2.9 50.0 -- 0.0 58242 55008 2770 94.4 0.2392 0.2392 0.2392 0.2829 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 2.9 3.0 -- 217 4473 0.3887 0.381 -- 81.5
X Ray Diffraction 3.0 3.12 -- 281 4907 0.3616 0.3867 -- 90.6
X Ray Diffraction 3.12 3.27 -- 279 5068 0.3349 0.3754 -- 92.6
X Ray Diffraction 3.27 3.44 -- 285 5156 0.2998 0.348 -- 94.1
X Ray Diffraction 3.44 3.65 -- 269 5218 0.2661 0.3183 -- 95.4
X Ray Diffraction 3.65 3.94 -- 262 5343 0.2415 0.2886 -- 96.7
X Ray Diffraction 3.94 4.33 -- 284 5378 0.2078 0.2538 -- 97.6
X Ray Diffraction 4.33 4.96 -- 303 5452 0.1852 0.2287 -- 98.4
X Ray Diffraction 4.96 6.24 -- 293 5503 0.2067 0.2696 -- 98.3
X Ray Diffraction 6.24 50.0 -- 297 5740 0.183 0.218 -- 98.6
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 61.8011
Anisotropic B[1][1] -4.782
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.663
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.119
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.537
c_mcangle_it 2.052
c_scbond_it 1.548
c_mcbond_it 1.155
c_angle_d 0.966
c_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 16623
Nucleic Acid Atoms 0
Heterogen Atoms 76
Solvent Atoms 149

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
Phaser Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
CNS refinement
HKL data reduction