X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.75
Temperature 303.0
Details 16% PEG6000, 0.5M NaCl, 25mM CaCl2, 5% methanol, 50mM HEPES, 50 mM Tris-HCl, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.67 α = 81.27
b = 59.71 β = 87.67
c = 101.54 γ = 88.39
Symmetry
Space Group P 1

Diffraction

Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 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
2.6 50 100.0 -- -- -- -- 34296 41067 2.0 2.0 --

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 2.6 42.404 -- 0.16 42680 33610 1978 96.22 -- 0.1874 0.1845 0.2446 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 2.6 2.661 -- 127 2449 0.2735 0.3934 -- 87.0
X Ray Diffraction 2.661 2.7329 -- 138 2641 0.2436 0.3204 -- 91.0
X Ray Diffraction 2.7329 2.8133 -- 136 2698 0.2561 0.3414 -- 93.0
X Ray Diffraction 2.8133 2.9041 -- 133 2729 0.2114 0.3524 -- 95.0
X Ray Diffraction 2.9041 3.0079 -- 146 2822 0.2247 0.3044 -- 96.0
X Ray Diffraction 3.0079 3.1283 -- 136 2807 0.1941 0.2904 -- 97.0
X Ray Diffraction 3.1283 3.2706 -- 148 2816 0.21 0.299 -- 98.0
X Ray Diffraction 3.2706 3.443 -- 144 2844 0.2021 0.2772 -- 98.0
X Ray Diffraction 3.443 3.6586 -- 147 2881 0.1862 0.2407 -- 99.0
X Ray Diffraction 3.6586 3.9409 -- 143 2866 0.1738 0.2036 -- 99.0
X Ray Diffraction 3.9409 4.3371 -- 145 2885 0.1566 0.2198 -- 99.0
X Ray Diffraction 4.3371 4.9638 -- 150 2906 0.1342 0.1991 -- 99.0
X Ray Diffraction 4.9638 6.2507 -- 146 2871 0.1761 0.1916 -- 99.0
X Ray Diffraction 6.2507 42.4101 -- 139 2874 0.1787 0.207 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -5.8585
Anisotropic B[1][2] -10.1317
Anisotropic B[1][3] -2.3552
Anisotropic B[2][2] -2.1152
Anisotropic B[2][3] 1.1218
Anisotropic B[3][3] 7.9737
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.085
f_dihedral_angle_d 16.23
f_angle_d 1.284
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9886
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 154

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHRNIX Structure Solution
PHENIX Structure Refinement
Software
Software Name Purpose
PHENIX refinement
PHRNIX model building
MAR345dtb data collection