X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 289.0
Details 14% peg8000, 0.1 M Tris, pH8.5, 1.2 M NaCl, 125mM KCl, 150mM Arg-HCl,20mM MgCl2, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.06 α = 90
b = 128.06 β = 90
c = 73.78 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2011-10-21
Diffraction Radiation
Monochromator Protocol
double-crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97915 APS 19-ID

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
2.15 50 99.7 0.064 0.056 -- 9.6 33951 33844 2.0 2.0 47.5
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)
2.15 2.19 100.0 0.819 0.743 3.2 9.4 1664

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 2.15 36.947 -- 1.34 34021 33793 1998 99.33 -- 0.2087 0.207 0.2338 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 2.1478 2.2015 -- 133 2119 0.2478 0.2806 -- 95.0
X Ray Diffraction 2.2015 2.261 -- 141 2239 0.2218 0.2138 -- 100.0
X Ray Diffraction 2.261 2.3275 -- 142 2267 0.2125 0.2404 -- 100.0
X Ray Diffraction 2.3275 2.4026 -- 139 2228 0.2028 0.2367 -- 100.0
X Ray Diffraction 2.4026 2.4885 -- 143 2258 0.214 0.264 -- 100.0
X Ray Diffraction 2.4885 2.5881 -- 141 2256 0.2096 0.2189 -- 100.0
X Ray Diffraction 2.5881 2.7058 -- 143 2264 0.2067 0.2405 -- 100.0
X Ray Diffraction 2.7058 2.8484 -- 143 2278 0.227 0.2963 -- 100.0
X Ray Diffraction 2.8484 3.0268 -- 143 2261 0.2243 0.3014 -- 100.0
X Ray Diffraction 3.0268 3.2604 -- 142 2285 0.2171 0.2375 -- 100.0
X Ray Diffraction 3.2604 3.5883 -- 144 2288 0.2072 0.264 -- 100.0
X Ray Diffraction 3.5883 4.1069 -- 147 2329 0.2003 0.2294 -- 100.0
X Ray Diffraction 4.1069 5.172 -- 147 2335 0.1771 0.1829 -- 100.0
X Ray Diffraction 5.172 36.9524 -- 150 2388 0.2215 0.2293 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -2.499
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.499
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.998
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.071
f_dihedral_angle_d 14.152
f_angle_d 1.17
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2485
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 71

Software

Computing
Computing Package Purpose
HKL-3000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7.1_743) 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.refine: 1.7.1_743) model building
HKL-3000 data collection