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 MgCl2, 0.067M NaCl, 0.1M Tris

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.08 α = 90
b = 81 β = 109.98
c = 58.01 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 -- 2014-04-25
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 1.000 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
2.24 50 99.4 0.108 -- 21.0 6.5 -- 22571 -- -- --
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)
2.24 2.28 99.9 0.631 -- -- 6.5 1117

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 2.24 45.79 -- 0.0 -- 21584 1914 95.08 -- 0.1957 0.1921 0.2322 --
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 2.2401 2.2961 -- 129 1238 0.2492 0.2972 -- 85.0
X Ray Diffraction 2.2961 2.3582 -- 125 1339 0.2333 0.2525 -- 90.0
X Ray Diffraction 2.3582 2.4276 -- 140 1337 0.2248 0.2578 -- 93.0
X Ray Diffraction 2.4276 2.5059 -- 130 1365 0.2214 0.2663 -- 93.0
X Ray Diffraction 2.5059 2.5955 -- 130 1401 0.227 0.2776 -- 94.0
X Ray Diffraction 2.5955 2.6994 -- 126 1412 0.2258 0.2666 -- 95.0
X Ray Diffraction 2.6994 2.8222 -- 133 1359 0.2288 0.2367 -- 93.0
X Ray Diffraction 2.8222 2.971 -- 137 1422 0.2123 0.2677 -- 96.0
X Ray Diffraction 2.971 3.1571 -- 151 1444 0.2107 0.2632 -- 98.0
X Ray Diffraction 3.1571 3.4008 -- 140 1456 0.2081 0.2429 -- 98.0
X Ray Diffraction 3.4008 3.7429 -- 136 1448 0.1875 0.2301 -- 99.0
X Ray Diffraction 3.7429 4.2841 -- 141 1461 0.1679 0.2035 -- 98.0
X Ray Diffraction 4.2841 5.3962 -- 149 1496 0.1576 0.2111 -- 100.0
X Ray Diffraction 5.3962 45.7997 -- 147 1492 0.1762 0.2084 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.003
f_chiral_restr 0.024
f_angle_d 0.668
f_dihedral_angle_d 12.8
f_plane_restr 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3850
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 121

Software

Software
Software Name Purpose
PHENIX refinement version: 1.9_1690
HKL-2000 data scaling
PDB_EXTRACT data extraction version: 3.15
HKL-2000 data reduction
PHENIX phasing