☰ Navigation Tabs
Crystal structure of apo leucyl aminopeptidase from Bacillus amyloliquefaciens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JRU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 0.5 M succinic acid (pH 7.0), 0.1 M Bis-Tris propane (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 4.78 74.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.245 α = 90 b = 200.245 β = 90 c = 89.022 γ = 120
Symmetry Space Group P 63 2 2
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 PILATUS3 S 2M 2019-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9793 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.748 50 99.24 0.996 21.69 30.3 27747
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.748 2.848 0.97
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3JRU 2.748 37.871 27669 1332 99.133 0.172 0.17 0.1705 0.2118 0.2115 58.642
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] -1.055 -0.527 -1.055 3.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.235 r_dihedral_angle_4_deg 24.148 r_dihedral_angle_3_deg 20.197 r_lrange_it 11.52 r_scangle_it 10.718 r_scbond_it 8.269 r_mcangle_it 7.512 r_dihedral_angle_1_deg 7.338 r_mcbond_it 5.573 r_angle_refined_deg 1.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.235 r_dihedral_angle_4_deg 24.148 r_dihedral_angle_3_deg 20.197 r_lrange_it 11.52 r_scangle_it 10.718 r_scbond_it 8.269 r_mcangle_it 7.512 r_dihedral_angle_1_deg 7.338 r_mcbond_it 5.573 r_angle_refined_deg 1.855 r_nbtor_refined 0.318 r_symmetry_nbd_refined 0.259 r_nbd_refined 0.242 r_symmetry_xyhbond_nbd_refined 0.227 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.139 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3714 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing