X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 298.0
Details The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor-diffusion sitting drop method. Crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at pH 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 M sodium citrate, pH 5.5, containing 10% v/v glycerol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.71 α = 90
b = 85.42 β = 90
c = 63.54 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2014-01-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 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
1.25 38.2 99.1 -- 0.029 12.444 6.3 64492 64492 -- -- --
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)
1.25 1.32 95.8 0.498 0.498 1.6 6.2 8993

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 1.25 63.54 -- -- -- 61174 3263 98.99 -- 0.1471 0.14575 0.17232 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 1.25 1.283 -- 219 4141 0.23 0.218 -- 91.73
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.421
Anisotropic B[1][1] -0.94
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.85
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.08
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 14.08
r_dihedral_angle_4_deg 19.002
r_long_range_B_refined 7.438
r_mcangle_it 2.692
r_scbond_other 3.692
r_angle_refined_deg 1.738
r_dihedral_angle_2_deg 31.893
r_mcbond_other 2.024
r_gen_planes_refined 0.011
r_scbond_it 3.693
r_mcangle_other 2.707
r_sphericity_bonded 13.42
r_chiral_restr 0.101
r_long_range_B_other 7.437
r_bond_refined_d 0.015
r_angle_other_deg 2.97
r_scangle_other 4.146
r_rigid_bond_restr 6.56
r_bond_other_d 0.0
r_dihedral_angle_1_deg 6.095
r_sphericity_free 59.37
r_gen_planes_other 0.014
r_mcbond_it 2.086
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1793
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 197

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0049
SCALA data scaling version: 3.3.15
PDB_EXTRACT data extraction version: 3.15