X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4
Temperature 289.0
Details TTR pH 4.0 crystals were grown in the presence of 0.1 M sodium acetate (pH 4.0), 100 mM KCl, 1 mM EDTA and 0.3-0.5 M ammonium sulfate which was equilibrated against 2 M ammonium sulfate in hanging drop, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.22 α = 90
b = 85.08 β = 90
c = 62.92 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 mirrors 2003-01-10
Diffraction Radiation
Monochromator Protocol
MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.541 -- --

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
1.72 22.19 99.68 -- -- -- -- 25276 25276 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)
1.72 1.76 97.1 -- -- -- -- --

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 1.72 22.19 0.0 0.0 25276 25276 1290 99.68 0.22276 0.22276 0.22129 0.24943 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 1.72 1.764 -- 86 1699 0.276 0.353 -- 97.12
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.27
Anisotropic B[1][1] -0.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.23
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 0.147
r_symmetry_hbond_refined 0.114
r_angle_other_deg 0.854
r_nbd_refined 0.179
r_nbtor_refined 0.174
r_bond_other_d 0.002
r_symmetry_vdw_other 0.242
r_scbond_it 1.78
r_symmetry_vdw_refined 0.212
r_nbtor_other 0.084
r_angle_refined_deg 1.353
r_chiral_restr 0.095
r_gen_planes_refined 0.004
r_xyhbond_nbd_refined 0.097
r_mcbond_it 1.094
r_nbd_other 0.194
r_dihedral_angle_2_deg 28.224
r_dihedral_angle_3_deg 13.35
r_dihedral_angle_4_deg 15.869
r_mcangle_it 1.198
r_dihedral_angle_1_deg 11.003
r_scangle_it 2.68
r_gen_planes_other 0.001
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1754
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 157

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
CrystalClear data collection
DENZO data reduction
SCALEPACK data scaling
EPMR phasing