X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details Crystals of recombinant WT TTR were obtained from protein solutions at 5 mg/ml (in 100 mM KCl, 100 mM phosphate [pH 7.4], 1 M ammonium sulfate) equilibrated against 2 M ammonium sulfate in hanging drop experiments. The TTR ligand complexes were prepared from crystals soaked for 2 weeks with a 10-fold molar excess , pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.24 α = 90
b = 85.84 β = 90
c = 64.79 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAC Science DIP-2030 -- 1999-06-07
Diffraction Radiation
Monochromator Protocol
MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU -- -- --

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
1.8 27.52 92.1 0.037 -- -- -- 21209 21209 0.0 0.0 --
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)
1.8 1.86 92.4 -- -- -- -- --

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 1.8 27.52 -- -- 21209 21209 1097 92.07 0.18199 0.18199 0.17998 0.21972 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 1.8 1.847 -- 74 1477 0.253 0.264 -- 92.76
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.923
Anisotropic B[1][1] 0.75
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.46
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.283
r_scbond_it 3.516
r_mcangle_it 2.124
r_mcbond_it 1.466
r_nbd_refined 0.218
r_gen_planes_refined 0.006
r_chiral_restr 0.104
r_dihedral_angle_4_deg 17.212
r_dihedral_angle_3_deg 14.674
r_dihedral_angle_2_deg 35.303
r_dihedral_angle_1_deg 5.365
r_angle_refined_deg 1.497
r_bond_refined_d 0.014
r_nbtor_refined 0.313
r_xyhbond_nbd_refined 0.2
r_symmetry_vdw_refined 0.26
r_symmetry_hbond_refined 0.311
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1750
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 120

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement
AMORE model building
SCALEPACK data reduction