X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 298.0
Details 30% PEG 1500, 100 mM sodium acetate, pH 5.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.3 α = 90
b = 108.3 β = 90
c = 49.66 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 ADSC QUANTUM 210r -- 2013-10-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.0 ALS 8.3.1

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
1.75 93.83 94.7 -- 0.049 -- 4.1 -- 31775 -- -- --
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)
1.749 1.94 79.5 0.112 -- 5.1 2.1 3808

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 1.749 43.888 -- 1.35 -- 31775 2033 94.17 -- 0.2151 0.2074 0.2396 --
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 1.7503 1.791 -- 105 1480 0.2901 0.3121 -- 67.0
X Ray Diffraction 1.791 1.8358 -- 117 1741 0.2729 0.3126 -- 77.0
X Ray Diffraction 1.8358 1.8854 -- 135 1982 0.2641 0.3015 -- 89.0
X Ray Diffraction 1.8854 1.9409 -- 113 1766 0.4255 0.5328 -- 80.0
X Ray Diffraction 1.9409 2.0036 -- 139 2106 0.2492 0.2726 -- 94.0
X Ray Diffraction 2.0036 2.0752 -- 137 2093 0.2317 0.3034 -- 94.0
X Ray Diffraction 2.0752 2.1583 -- 142 2106 0.2281 0.2062 -- 94.0
X Ray Diffraction 2.1583 2.2565 -- 117 1815 0.302 0.3383 -- 81.0
X Ray Diffraction 2.2565 2.3754 -- 138 2026 0.2142 0.2368 -- 91.0
X Ray Diffraction 2.3754 2.5243 -- 142 2109 0.2094 0.2655 -- 94.0
X Ray Diffraction 2.5243 2.7191 -- 142 2094 0.2108 0.228 -- 94.0
X Ray Diffraction 2.7191 2.9927 -- 145 2099 0.2032 0.2726 -- 94.0
X Ray Diffraction 2.9927 3.4256 -- 141 2130 0.1782 0.1996 -- 94.0
X Ray Diffraction 3.4256 4.3153 -- 142 2095 0.1518 0.174 -- 93.0
X Ray Diffraction 4.3153 43.9015 -- 139 2113 0.1905 0.2494 -- 90.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.26
Anisotropic B[1][1] 0.0131
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0131
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.0262
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 2.39
f_chiral_restr 0.448
f_plane_restr 0.007
f_dihedral_angle_d 38.816
f_bond_d 0.024
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2335
Nucleic Acid Atoms 0
Heterogen Atoms 276
Solvent Atoms 312

Software

Software
Software Name Purpose
SCALA data scaling
PHASER phasing
PHENIX refinement version: 1.6.4_486
PDB_EXTRACT data extraction version: 3.20
MOSFLM data reduction