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 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.97 α = 90
b = 85.16 β = 90
c = 64.13 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M Rh coated flat mirror 2012-04-06
Diffraction Radiation
Monochromator Protocol
Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.9795 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
1.45 85.16 99.9 -- 0.044 -- 8.2 -- 42818 -- -- 20.4
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)
1.45 1.5 100.0 -- 0.519 3.7 8.1 4221

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 1.45 85.16 -- 0.0 -- 42350 2139 99.56 -- 0.1665 0.1654 0.1873 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 1.45 1.488 -- 164 2968 0.269 0.338 -- 99.75
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.2489
Anisotropic B[1][1] 0.6
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.25
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.017
r_mcbond_it 2.198
r_rigid_bond_restr 1.904
r_dihedral_angle_1_deg 6.211
r_gen_planes_other 0.005
r_mcangle_it 3.596
r_angle_refined_deg 1.727
r_dihedral_angle_4_deg 20.317
r_chiral_restr 0.109
r_scangle_it 7.076
r_bond_other_d 0.001
r_gen_planes_refined 0.01
r_angle_other_deg 0.954
r_dihedral_angle_2_deg 34.154
r_dihedral_angle_3_deg 14.591
r_scbond_it 4.696
r_mcbond_other 0.619
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1785
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 82

Software

Software
Software Name Purpose
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11