3NX0

Hinge-loop mutation can be used to control 3D domain swapping and amyloidogenesis of human cystatin C


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52920.1 M sodium cacodylate, 0.2 M ammonium sulfate and 25% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
3.0759.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.316α = 90
b = 76.316β = 90
c = 97.723γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2008-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.81272EMBL/DESY, HamburgX11

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
12.043095.80.07820.56.820617
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)
2.042.1171.30.4292.13.81451

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 REPLACEMENTTHROUGHOUT2.04301870399895.710.181370.178990.22474RANDOM11.671
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]
0.80.40.8-1.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.222
r_dihedral_angle_4_deg18.583
r_dihedral_angle_3_deg15.789
r_dihedral_angle_1_deg7.772
r_scangle_it4.551
r_scbond_it2.823
r_angle_refined_deg1.836
r_mcangle_it1.593
r_mcbond_it0.93
r_chiral_restr0.248
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.222
r_dihedral_angle_4_deg18.583
r_dihedral_angle_3_deg15.789
r_dihedral_angle_1_deg7.772
r_scangle_it4.551
r_scbond_it2.823
r_angle_refined_deg1.836
r_mcangle_it1.593
r_mcbond_it0.93
r_chiral_restr0.248
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_bond_other_d
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_sphericity_bonded
r_mcbond_other
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1722
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms10

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling