X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 282.0
Details Protein solution was at 10 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl and 50 mM imidazole. Mother liqueur contained 0.2 M ammonium chloride, 0.01 M calcium chloride dihydrate, 0.05 M Tris (pH 8.5), 30% PEG 4,000. Cryoprotectant was 13% glycerol, vapor diffusion, sitting drop, temperature 282K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.32 α = 90
b = 97.13 β = 90
c = 144.1 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 RAYONIX MX-225 -- 2012-03-23
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 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 30 99.6 0.088 -- -- 7.6 45647 45465 0.0 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)
2.0 2.07 99.8 0.777 -- -- 7.1 --

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
MOLECULAR REPLACEMENT 2.003 29.533 -- 1.36 45600 41885 2112 91.89 -- 0.1675 0.1648 0.2177 --
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 2.003 2.0496 -- 89 1516 0.1924 0.2502 -- 54.0
X Ray Diffraction 2.0496 2.1009 -- 116 1836 0.1859 0.2944 -- 66.0
X Ray Diffraction 2.1009 2.1576 -- 114 2274 0.1898 0.2539 -- 79.0
X Ray Diffraction 2.1576 2.2211 -- 131 2522 0.1719 0.2649 -- 89.0
X Ray Diffraction 2.2211 2.2928 -- 145 2709 0.1679 0.2202 -- 95.0
X Ray Diffraction 2.2928 2.3747 -- 161 2772 0.1797 0.2474 -- 97.0
X Ray Diffraction 2.3747 2.4697 -- 135 2838 0.1756 0.232 -- 99.0
X Ray Diffraction 2.4697 2.5821 -- 167 2771 0.1741 0.2299 -- 99.0
X Ray Diffraction 2.5821 2.7181 -- 161 2864 0.1813 0.2709 -- 100.0
X Ray Diffraction 2.7181 2.8883 -- 123 2893 0.1847 0.2247 -- 100.0
X Ray Diffraction 2.8883 3.111 -- 144 2895 0.1858 0.226 -- 100.0
X Ray Diffraction 3.111 3.4237 -- 134 2925 0.1768 0.2542 -- 100.0
X Ray Diffraction 3.4237 3.9181 -- 150 2927 0.1585 0.1992 -- 100.0
X Ray Diffraction 3.9181 4.9327 -- 161 2952 0.13 0.1713 -- 100.0
X Ray Diffraction 4.9327 29.536 -- 181 3079 0.1536 0.1928 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.7191
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.4606
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.7415
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.075
f_dihedral_angle_d 15.668
f_angle_d 1.172
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5100
Nucleic Acid Atoms 0
Heterogen Atoms 92
Solvent Atoms 387

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
SCALEPACK data reduction
DENZO data collection