X-RAY DIFFRACTION Experimental Data & Validation


Lost? View more X-Ray Crystallographic info.

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 24%(w/v)PEG4000,50mM MgCl2,100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.09 α = 90
b = 78.09 β = 90
c = 397.54 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2012-01-01
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 1.033 APS 21-ID-F

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
2.8 50 99.9 0.114 -- -- 9.0 33600 33519 -- -- 40.3
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)
2.8 2.85 100.0 0.171 -- 18.1 4.6 1634

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 2.8 40.045 -- 1.91 -- 33489 2026 99.87 -- 0.2594 0.2562 0.3068 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 2.8003 2.8703 -- 145 2234 0.2964 0.3626 -- 100.0
X Ray Diffraction 2.8703 2.9478 -- 145 2233 0.299 0.3564 -- 100.0
X Ray Diffraction 2.9478 3.0346 -- 144 2251 0.2832 0.3523 -- 100.0
X Ray Diffraction 3.0346 3.1325 -- 143 2274 0.2856 0.3742 -- 100.0
X Ray Diffraction 3.1325 3.2444 -- 143 2237 0.2822 0.3457 -- 100.0
X Ray Diffraction 3.2444 3.3742 -- 148 2246 0.267 0.3305 -- 100.0
X Ray Diffraction 3.3742 3.5277 -- 145 2231 0.2772 0.3105 -- 100.0
X Ray Diffraction 3.5277 3.7136 -- 147 2267 0.2596 0.3561 -- 100.0
X Ray Diffraction 3.7136 3.946 -- 138 2232 0.243 0.3148 -- 100.0
X Ray Diffraction 3.946 4.2504 -- 151 2244 0.2264 0.2945 -- 100.0
X Ray Diffraction 4.2504 4.6776 -- 145 2247 0.2131 0.2497 -- 100.0
X Ray Diffraction 4.6776 5.353 -- 142 2252 0.2245 0.2907 -- 100.0
X Ray Diffraction 5.353 6.7391 -- 144 2252 0.2783 0.3044 -- 100.0
X Ray Diffraction 6.7391 40.0494 -- 146 2263 0.2586 0.2402 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.7
Anisotropic B[1][1] 4.9635
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.9635
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -9.2344
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.059
f_dihedral_angle_d 17.386
f_angle_d 0.906
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6806
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 116

Software

Computing
Computing Package Purpose
MC-2 diffractometer software from EMBL Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Phnix.autoMR Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
Phnix.autoMR model building
MC-2 version: diffractometer software from EMBL data collection