X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 12% PEG8000, 0.1 M Tris, 1.9 M NaCl, 250mM KCl, 400mM Arg-HCl,2mM MgCl2, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.08 α = 90
b = 128.08 β = 90
c = 74.04 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 -- 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
2.6 50 99.9 0.074 0.087 -- 8.4 19456 19442 2.0 2.0 --
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)
2.6 2.64 100.0 0.877 0.746 2.31 8.4 958

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 2.602 40.502 -- 0.13 19454 19328 991 99.35 -- 0.2288 0.2264 0.2761 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 2.6015 2.7387 -- 141 2529 0.2852 0.3605 -- 98.0
X Ray Diffraction 2.7387 2.9102 -- 154 2536 0.272 0.3672 -- 100.0
X Ray Diffraction 2.9102 3.1348 -- 133 2589 0.2513 0.2848 -- 99.0
X Ray Diffraction 3.1348 3.4502 -- 153 2592 0.2419 0.3096 -- 99.0
X Ray Diffraction 3.4502 3.949 -- 148 2603 0.2259 0.2581 -- 100.0
X Ray Diffraction 3.949 4.9739 -- 141 2661 0.1996 0.2459 -- 100.0
X Ray Diffraction 4.9739 40.507 -- 121 2827 0.2209 0.2616 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.261
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.261
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.522
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.085
f_dihedral_angle_d 16.183
f_angle_d 1.37
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2505
Nucleic Acid Atoms 0
Heterogen Atoms 57
Solvent Atoms 2

Software

Computing
Computing Package Purpose
HKL-2000 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-2000 data collection