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 1 uL mother liquor + 1 uL TTR 10 mg/mL; crystals appeared in about 5 days, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.17 α = 90
b = 86.11 β = 90
c = 63.76 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 2005-05-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU ULTRAX 18 1.542 -- --

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
1.6 86.11 99.9 0.046 0.046 -- 6.9 32087 32073 2.0 2.0 20.5
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)
1.6 1.69 100.0 0.398 0.398 1.9 6.7 4565

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 1.6 17.87 -- 0.0 32061 32042 1624 99.96 0.192 0.192 0.191 0.218 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 1.6 1.641 -- 120 2153 0.328 0.314 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.203
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.181
r_dihedral_angle_4_deg 15.355
r_xyhbond_nbd_refined 0.119
r_nbtor_refined 0.301
r_symmetry_hbond_refined 0.103
r_chiral_restr 0.072
r_gen_planes_refined 0.003
r_dihedral_angle_2_deg 30.885
r_angle_refined_deg 1.057
r_dihedral_angle_3_deg 13.435
r_dihedral_angle_1_deg 5.758
r_symmetry_vdw_refined 0.18
r_bond_refined_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1955
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 282

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