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 with inhibitors 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, vapor diffusion, sitting drop, temperature 298.0, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.63 α = 90
b = 86.06 β = 90
c = 62.8 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING) 2012-08-02
Diffraction Radiation
Monochromator Protocol
ASYMMETRIC CUT 4.965 DEGS SIDE SCATTERING BENT CUBE-ROOT I -BEAM SINGLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.9797 SSRL BL12-2

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
1.5 37.48 98.5 -- 0.059 -- 6.1 -- 36103 -- -- 12.6
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)
1.5 1.58 95.7 -- 0.537 5.9 5.9 5007

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 1.5 37.48 -- 0.0 -- 36009 1796 97.95 -- 0.1615 0.1602 0.1852 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 1.502 1.541 -- 129 2310 0.22 0.28 -- 91.31
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.9124
Anisotropic B[1][1] 0.51
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.4
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.11
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.592
r_sphericity_free 29.216
r_sphericity_bonded 12.428
r_bond_refined_d 0.014
r_rigid_bond_restr 17.386
r_bond_other_d 0.001
r_angle_other_deg 3.6
r_mcbond_other 2.905
r_dihedral_angle_1_deg 6.215
r_mcbond_it 2.963
r_gen_planes_other 0.096
r_dihedral_angle_4_deg 19.742
r_mcangle_it 3.607
r_gen_planes_refined 0.048
r_chiral_restr 0.103
r_dihedral_angle_3_deg 15.944
r_dihedral_angle_2_deg 30.794
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1785
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 138

Software

Software
Software Name Purpose
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
Blu-Ice data collection
XDS data reduction
XDS data scaling
PHASER phasing