X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 298.0
Details 100 mM sodium citrate, pH5.5, 15% PEG3350, 10%DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.47 α = 90
b = 65.95 β = 90
c = 72.01 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9793376 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
2.29 50 99.9 0.121 -- -- 6.9 -- 11548 -- -- --
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)
2.29 2.33 100.0 0.503 -- -- 7.2 --

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 2.291 40.577 -- 1.33 -- 10368 502 89.94 -- 0.1843 0.1804 0.2598 --
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 2.2905 2.521 -- 89 1805 0.1919 0.2727 -- 67.0
X Ray Diffraction 2.521 2.8857 -- 149 2510 0.2122 0.3197 -- 93.0
X Ray Diffraction 2.8857 3.6353 -- 132 2718 0.1802 0.2959 -- 100.0
X Ray Diffraction 3.6353 40.5831 -- 132 2833 0.1671 0.2111 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.9029
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.05
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.008
f_angle_d 1.145
f_chiral_restr 0.061
f_plane_restr 0.005
f_dihedral_angle_d 17.041
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1910
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 93

Software

Software
Software Name Purpose
PHENIX refinement version: 1.8.1_1168
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
HKL-3000 data collection
DENZO data reduction