5L6Q

Refolded AL protein from cardiac amyloidosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4OD2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1 M MES, 18% PEG 8000, 0.1 M Zinc acetate
Crystal Properties
Matthews coefficientSolvent content
2.243

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.02α = 90
b = 105.81β = 90
c = 34.75γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
11.43097.60.05412.6442100
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)
11.41.598.70.5252.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT4OD21.41039847209897.390.149040.147260.18208RANDOM17.965
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]
-0.890.260.62
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.438
r_dihedral_angle_2_deg35.586
r_dihedral_angle_4_deg13.53
r_sphericity_bonded11.764
r_dihedral_angle_3_deg11.079
r_dihedral_angle_1_deg6.472
r_long_range_B_refined5.083
r_long_range_B_other3.594
r_scangle_other3.043
r_scbond_it2.584
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.438
r_dihedral_angle_2_deg35.586
r_dihedral_angle_4_deg13.53
r_sphericity_bonded11.764
r_dihedral_angle_3_deg11.079
r_dihedral_angle_1_deg6.472
r_long_range_B_refined5.083
r_long_range_B_other3.594
r_scangle_other3.043
r_scbond_it2.584
r_scbond_other2.584
r_rigid_bond_restr2.201
r_mcangle_it2.184
r_mcangle_other2.184
r_mcbond_it1.88
r_mcbond_other1.81
r_angle_refined_deg1.668
r_angle_other_deg0.981
r_chiral_restr0.108
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1604
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing