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% PEG 3350, 0.05M magnesium chloride, 0.067M sodium chloride, 0.1M Tris, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.17 α = 90
b = 81.09 β = 109.49
c = 58.12 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
PIXEL DECTRIS PILATUS 6M -- 2012-07-27
Diffraction Radiation
Monochromator Protocol
Side scattering bent cube I-beam single crystal, asymmetric cut 4.965 degs SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 1.0 SSRL BL11-1

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
2.04 50 97.12 -- 0.117 -- 6.3 29476 29476 1.0 1.0 33.72
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)
2.0375 2.09 89.33 -- 0.812 2.3 6.2 --

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 2.0375 45.735 -- 0.0 27626 27626 1874 91.02 0.2108 0.2108 0.2081 0.2468 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 2.0375 2.0926 -- 108 1587 0.2948 0.369 -- 73.0
X Ray Diffraction 2.0926 2.1542 -- 140 1799 0.2664 0.2972 -- 84.0
X Ray Diffraction 2.1542 2.2237 -- 136 1752 0.2519 0.2726 -- 81.0
X Ray Diffraction 2.2237 2.3032 -- 130 1875 0.2771 0.3563 -- 87.0
X Ray Diffraction 2.3032 2.3954 -- 154 2029 0.2306 0.2829 -- 93.0
X Ray Diffraction 2.3954 2.5044 -- 149 2045 0.219 0.2796 -- 94.0
X Ray Diffraction 2.5044 2.6364 -- 144 2088 0.231 0.2706 -- 95.0
X Ray Diffraction 2.6364 2.8016 -- 149 1996 0.2209 0.2936 -- 93.0
X Ray Diffraction 2.8016 3.0178 -- 159 2110 0.2108 0.2743 -- 97.0
X Ray Diffraction 3.0178 3.3215 -- 154 2120 0.2135 0.2497 -- 98.0
X Ray Diffraction 3.3215 3.8019 -- 154 2085 0.1843 0.2112 -- 95.0
X Ray Diffraction 3.8019 4.7891 -- 144 2095 0.1628 0.169 -- 95.0
X Ray Diffraction 4.7891 45.7462 -- 153 2171 0.2115 0.2513 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.79
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.5104
Anisotropic B[2][2] 4.064
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.274
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_chiral_restr 0.039
f_dihedral_angle_d 14.365
f_angle_d 0.553
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3917
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 165

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX (phenix.automr) Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
PHENIX version: (phenix.automr) model building
HKL-2000 data collection