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_angle_refined_deg 1.08
r_symmetry_hbond_refined 0.131
r_dihedral_angle_1_deg 5.657
r_nbtor_refined 0.305
r_dihedral_angle_3_deg 13.654
r_dihedral_angle_4_deg 14.584
r_chiral_restr 0.069
r_scangle_it 1.522
r_bond_refined_d 0.007
r_nbd_refined 0.195
r_mcangle_it 0.862
r_scbond_it 0.985
r_gen_planes_refined 0.003
r_dihedral_angle_2_deg 31.38
r_mcbond_it 0.481
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

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.004
MAR345dtb data collection