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Crystal structure of isoaspartyl dipeptidase from Leucothrix mucor DSM2157
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.56 M NaH2PO4 and 1.04 M K2HPO4
Crystal Properties Matthews coefficient Solvent content 3.3 62.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.493 α = 90 b = 163.691 β = 90 c = 170.453 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2021-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9792 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 118.34 98.2 0.1 0.999 9.68 13.6 386931
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 97.5 0.868 0.895 0.56 13.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 118.34 368266 18699 98.16 0.16724 0.16624 0.1758 0.18695 0.1956 RANDOM 29.635
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] 0.45 -0.88 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.638 r_dihedral_angle_4_deg 15.745 r_dihedral_angle_3_deg 11.485 r_long_range_B_refined 7.503 r_long_range_B_other 7.243 r_dihedral_angle_1_deg 7.006 r_scangle_other 6.444 r_scbond_it 4.547 r_scbond_other 4.511 r_mcangle_it 3.742
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.638 r_dihedral_angle_4_deg 15.745 r_dihedral_angle_3_deg 11.485 r_long_range_B_refined 7.503 r_long_range_B_other 7.243 r_dihedral_angle_1_deg 7.006 r_scangle_other 6.444 r_scbond_it 4.547 r_scbond_other 4.511 r_mcangle_it 3.742 r_mcangle_other 3.742 r_mcbond_it 2.571 r_mcbond_other 2.571 r_angle_refined_deg 1.614 r_angle_other_deg 1.411 r_chiral_restr 0.073 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 22786 Nucleic Acid Atoms Solvent Atoms 3053 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing