X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details Protein Solution (5.0 mg/ml protein, 0.05 M NaCl, 0.0003 M NaN3, and 0.005 M HEPES pH 7) mixed in a 1:1 ratio with the Well Solution (0.157 M (NH4)2HPO4, 2.143 M (NH4)H2PO4, and 0.1 M Tris pH 8.0). Cryoprotected with 0.157 M (NH4)2HPO4, 2.143 M (NH4)H2PO4, 5% ethylene glycol, and 0.1 M Tris pH 8.0, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.26 α = 90
b = 122.06 β = 90
c = 182 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARmosaic 300 mirrors and beryllium lenses 2009-11-19
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G

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
2.4 50 99.5 0.127 -- -- 6.2 -- 73974 -- -- --
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)
2.4 2.46 97.6 0.42 -- -- 5.3 4772

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 2.4 34.326 -- 0.0 -- 70898 3535 95.02 -- 0.1536 0.1508 0.2083 --
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 2.3846 2.4173 -- 106 2082 0.1973 0.2449 -- 75.0
X Ray Diffraction 2.4173 2.4518 -- 128 2492 0.1948 0.2677 -- 88.0
X Ray Diffraction 2.4518 2.4884 -- 132 2470 0.1903 0.2928 -- 89.0
X Ray Diffraction 2.4884 2.5273 -- 140 2531 0.1872 0.2685 -- 90.0
X Ray Diffraction 2.5273 2.5687 -- 131 2533 0.181 0.2645 -- 91.0
X Ray Diffraction 2.5687 2.613 -- 133 2598 0.191 0.2492 -- 92.0
X Ray Diffraction 2.613 2.6605 -- 135 2581 0.191 0.2518 -- 92.0
X Ray Diffraction 2.6605 2.7116 -- 134 2635 0.2018 0.2739 -- 93.0
X Ray Diffraction 2.7116 2.767 -- 139 2621 0.2068 0.2768 -- 94.0
X Ray Diffraction 2.767 2.8271 -- 140 2635 0.1937 0.3156 -- 94.0
X Ray Diffraction 2.8271 2.8928 -- 139 2685 0.1884 0.2419 -- 94.0
X Ray Diffraction 2.8928 2.9651 -- 139 2689 0.1901 0.2726 -- 95.0
X Ray Diffraction 2.9651 3.0453 -- 144 2709 0.1846 0.2582 -- 96.0
X Ray Diffraction 3.0453 3.1348 -- 148 2737 0.1804 0.245 -- 97.0
X Ray Diffraction 3.1348 3.2359 -- 146 2736 0.1686 0.2223 -- 98.0
X Ray Diffraction 3.2359 3.3515 -- 141 2787 0.1678 0.2221 -- 98.0
X Ray Diffraction 3.3515 3.4855 -- 146 2800 0.1579 0.2182 -- 99.0
X Ray Diffraction 3.4855 3.644 -- 147 2814 0.1527 0.197 -- 99.0
X Ray Diffraction 3.644 3.8359 -- 149 2817 0.1262 0.1837 -- 99.0
X Ray Diffraction 3.8359 4.0759 -- 149 2832 0.1217 0.1617 -- 99.0
X Ray Diffraction 4.0759 4.39 -- 152 2869 0.1096 0.1603 -- 99.0
X Ray Diffraction 4.39 4.8307 -- 149 2844 0.106 0.155 -- 100.0
X Ray Diffraction 4.8307 5.5272 -- 153 2907 0.1108 0.1728 -- 100.0
X Ray Diffraction 5.5272 6.9542 -- 154 2922 0.1355 0.1729 -- 100.0
X Ray Diffraction 6.9542 34.3294 -- 161 3037 0.143 0.1769 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.1839
Anisotropic B[1][1] -4.0662
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.8791
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.1871
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.933
f_dihedral_angle_d 13.991
f_plane_restr 0.003
f_bond_d 0.006
f_chiral_restr 0.069
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13126
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 692

Software

Software
Software Name Purpose
SCALEPACK data scaling
PHASER phasing
PHENIX refinement version: 1.6.4_486
PDB_EXTRACT data extraction version: 3.10
DENZO data reduction