X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details CRYSTALLIZATION CONDITIONS: 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 = 43.08 α = 90
b = 85.46 β = 90
c = 64.24 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 -- 1999-07-31
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
1.85 27.42 90.5 0.036 -- -- -- 18746 18746 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)
1.85 1.898 87.52 -- -- -- -- --

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 1.85 27.42 -- -- 18746 17787 959 89.65 0.21586 0.21586 0.21375 0.25745 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 1.85 1.898 -- 81 1244 0.268 0.278 -- 87.52
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.503
Anisotropic B[1][1] 0.62
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.3
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.32
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.924
r_scbond_it 2.646
r_mcangle_it 1.823
r_mcbond_it 1.253
r_nbd_refined 0.238
r_gen_planes_refined 0.035
r_chiral_restr 0.085
r_dihedral_angle_4_deg 14.689
r_dihedral_angle_3_deg 14.8
r_dihedral_angle_2_deg 40.347
r_dihedral_angle_1_deg 5.593
r_angle_refined_deg 1.496
r_bond_refined_d 0.011
r_nbtor_refined 0.324
r_xyhbond_nbd_refined 0.17
r_symmetry_vdw_refined 0.229
r_symmetry_hbond_refined 0.796
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1770
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 51

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
HKL-2000 data collection