5NBV

Crystal structure of native alpha-1-antitrypsin with seven stabilising mutations


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NBU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG 4000, carboxylic acid mixture
Crystal Properties
Matthews coefficientSolvent content
2.3246.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.7α = 90
b = 39.26β = 104.08
c = 90.56γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2013-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97630DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7352.8599.87.43.140844

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 REPLACEMENTTHROUGHOUT5NBU1.7352.8538771205699.610.218650.216450.25931RANDOM33.987
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]
-0.91.4-0.40.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.108
r_dihedral_angle_4_deg21.095
r_dihedral_angle_3_deg13.461
r_dihedral_angle_1_deg11.492
r_long_range_B_refined8.433
r_long_range_B_other8.433
r_scangle_other6.661
r_mcangle_it5.428
r_mcangle_other5.427
r_scbond_it4.717
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.108
r_dihedral_angle_4_deg21.095
r_dihedral_angle_3_deg13.461
r_dihedral_angle_1_deg11.492
r_long_range_B_refined8.433
r_long_range_B_other8.433
r_scangle_other6.661
r_mcangle_it5.428
r_mcangle_other5.427
r_scbond_it4.717
r_scbond_other4.716
r_mcbond_it4.046
r_mcbond_other4.041
r_angle_refined_deg0.581
r_angle_other_deg0.456
r_chiral_restr0.044
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d
r_gen_planes_other
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2789
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing