X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 291.0
Details mother liquor: 100 mM Tris, pH 7.5, 100 mM KCl, 20 % v/v PEG 400; drop consisting of 1 uL mother liquor and 1 uL wtTTR 10 mg/mL; crystals appeared in about 5 days; complex obtained by soaking in mother liquor supplemented with saturating amount of ligand., VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.3 α = 90
b = 86.5 β = 90
c = 63.46 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate Osmic 2005-06-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU ULTRAX 18 1.5418 -- --

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
1.87 51.17 93.5 0.043 0.043 -- 7.2 19713 19329 2.0 2.0 17.7
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)
1.87 1.96 79.8 0.184 0.184 4.1 6.9 2361

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 1.87 26.25 -- 0.0 19713 19297 994 94.87 0.203 0.203 0.2 0.245 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 1.87 1.918 -- 67 1238 0.22 0.27 -- 88.53
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.107
Anisotropic B[1][1] -0.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.02
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.522
r_scbond_it 0.985
r_mcangle_it 0.862
r_mcbond_it 0.481
r_symmetry_hbond_refined 0.131
r_bond_refined_d 0.007
r_angle_refined_deg 1.08
r_dihedral_angle_1_deg 5.657
r_dihedral_angle_2_deg 31.38
r_dihedral_angle_3_deg 13.654
r_dihedral_angle_4_deg 14.584
r_chiral_restr 0.069
r_gen_planes_refined 0.003
r_nbd_refined 0.195
r_nbtor_refined 0.305
r_xyhbond_nbd_refined 0.123
r_symmetry_vdw_refined 0.183
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.064
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1778
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 199

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.004 data extraction
REFMAC5 refinement
MOLREP molecular replacement
SCALA data processing
Mosflm collection/data indexing