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Crystal structure of native alpha-1-antitrypsin with seven stabilising mutations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NBU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 4000, carboxylic acid mixture
Crystal Properties Matthews coefficient Solvent content 2.32 46.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.7 α = 90 b = 39.26 β = 104.08 c = 90.56 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2013-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97630 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.73 52.85 99.8 7.4 3.1 40844
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5NBU 1.73 52.85 38771 2056 99.61 0.21865 0.21645 0.2226 0.25931 0.264 RANDOM 33.987
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] -0.9 1.4 -0.4 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.108 r_dihedral_angle_4_deg 21.095 r_dihedral_angle_3_deg 13.461 r_dihedral_angle_1_deg 11.492 r_long_range_B_refined 8.433 r_long_range_B_other 8.433 r_scangle_other 6.661 r_mcangle_it 5.428 r_mcangle_other 5.427 r_scbond_it 4.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.108 r_dihedral_angle_4_deg 21.095 r_dihedral_angle_3_deg 13.461 r_dihedral_angle_1_deg 11.492 r_long_range_B_refined 8.433 r_long_range_B_other 8.433 r_scangle_other 6.661 r_mcangle_it 5.428 r_mcangle_other 5.427 r_scbond_it 4.717 r_scbond_other 4.716 r_mcbond_it 4.046 r_mcbond_other 4.041 r_angle_refined_deg 0.581 r_angle_other_deg 0.456 r_chiral_restr 0.044 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 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 Atoms Number Protein Atoms 2789 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing