☰ Navigation Tabs
Crystal structure of mutant aspartase from Caenibacillus caldisaponilyticus in the closed loop conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R6V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2 M MgCl2, 0.1 M Tris pH 8.5, and 20% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.25 62.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.182 α = 90 b = 164.182 β = 90 c = 86.819 γ = 120
Symmetry Space Group P 32 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 PILATUS3 6M 2022-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9654 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.1 47.44 99.9 0.364 0.377 0.097 0.995 8.9 14.7 24734
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.31 100 2.342 2.428 0.637 0.578 14.3
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 3.1 47.44 23470 1241 99.92 0.20685 0.2041 0.2197 0.25891 0.2634 RANDOM 84.845
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] 2.18 1.09 2.18 -7.07
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.8 r_long_range_B_other 15.8 r_dihedral_angle_3_deg 15.512 r_scangle_other 11.847 r_mcangle_it 10.689 r_mcangle_other 10.689 r_scbond_it 7.471 r_scbond_other 7.47 r_dihedral_angle_2_deg 7.407 r_mcbond_it 7.023
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.8 r_long_range_B_other 15.8 r_dihedral_angle_3_deg 15.512 r_scangle_other 11.847 r_mcangle_it 10.689 r_mcangle_other 10.689 r_scbond_it 7.471 r_scbond_other 7.47 r_dihedral_angle_2_deg 7.407 r_mcbond_it 7.023 r_mcbond_other 7.023 r_dihedral_angle_1_deg 6.622 r_angle_refined_deg 1.505 r_angle_other_deg 0.516 r_chiral_restr 0.072 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 7125 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction