3MD5

Prion peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1 M Bis-Tris pH 6.5, 0.3 M ammonium acetate, 30-40% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.5319.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 19.618α = 90
b = 9.459β = 92.92
c = 19.672γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.91840APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.45084.10.05729.310.11309
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4561.70.1335.592

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.419.6513086284.010.1880.1860.232RANDOM10.844
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.54-0.88-1.241.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.731
r_dihedral_angle_1_deg6.733
r_sphericity_free6.251
r_dihedral_angle_2_deg6.223
r_sphericity_bonded3.979
r_scangle_it3.661
r_mcangle_it2.751
r_scbond_it2.55
r_rigid_bond_restr1.834
r_mcbond_it1.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.731
r_dihedral_angle_1_deg6.733
r_sphericity_free6.251
r_dihedral_angle_2_deg6.223
r_sphericity_bonded3.979
r_scangle_it3.661
r_mcangle_it2.751
r_scbond_it2.55
r_rigid_bond_restr1.834
r_mcbond_it1.66
r_angle_refined_deg1.432
r_chiral_restr0.118
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms84
Nucleic Acid Atoms
Solvent Atoms5
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction