X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.3
Temperature 294.0
Details 15% PEG3350, 0.05 M magnesium chloride, 0.067 M sodium chloride, 0.1 M Tris, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.11 α = 90
b = 84.19 β = 108.35
c = 58.48 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-12-18
Diffraction Radiation
Monochromator Protocol
Double crystal cryo-cooled Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 0.9 APS 23-ID-B

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
1.93 33.54 98.68 0.05 -- -- 3.5 38369 38369 1.0 1.0 --
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)
1.929 2.0 89.1 0.45 -- 2.1 2.0 3443

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 1.929 33.541 -- 0.0 38369 36236 1883 93.22 0.1779 0.1779 0.1766 0.2018 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 1.929 1.9816 -- 106 2060 0.2419 0.2795 -- 73.0
X Ray Diffraction 1.9816 2.0399 -- 117 2350 0.2118 0.2359 -- 84.0
X Ray Diffraction 2.0399 2.1057 -- 145 2517 0.1905 0.2391 -- 89.0
X Ray Diffraction 2.1057 2.181 -- 149 2628 0.1884 0.2131 -- 93.0
X Ray Diffraction 2.181 2.2683 -- 136 2436 0.2095 0.2609 -- 87.0
X Ray Diffraction 2.2683 2.3715 -- 134 2676 0.1809 0.2081 -- 95.0
X Ray Diffraction 2.3715 2.4965 -- 161 2735 0.1786 0.2415 -- 97.0
X Ray Diffraction 2.4965 2.6528 -- 153 2793 0.1801 0.2294 -- 98.0
X Ray Diffraction 2.6528 2.8575 -- 157 2763 0.1888 0.2342 -- 99.0
X Ray Diffraction 2.8575 3.1449 -- 153 2836 0.1789 0.2047 -- 100.0
X Ray Diffraction 3.1449 3.5995 -- 152 2837 0.1728 0.206 -- 100.0
X Ray Diffraction 3.5995 4.5333 -- 161 2851 0.1484 0.1515 -- 100.0
X Ray Diffraction 4.5333 33.5459 -- 159 2871 0.1745 0.179 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 1.1438
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 6.6831
Anisotropic B[2][2] 2.76
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.9038
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.002
f_chiral_restr 0.044
f_dihedral_angle_d 12.908
f_angle_d 0.614
f_plane_restr 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3937
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 323

Software

Software
Software Name Purpose
HKL-2000 data collection
PHENIX model building version: (phenix.automr)
PHENIX refinement version: (phenix.refine: 1.7.1_743)
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing