☰ Navigation Tabs
Crystallization and structural analyses of ZgHAD, a L-2-haloacid dehalogenase from the marine Flavobacterium Zobellia galactanivorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ASZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 25% (w/v) PEG3350, 0.1 M Tris-HCl pH 8.5 and 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.13 42.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.165 α = 90 b = 132.789 β = 92.31 c = 275.698 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 9M 2019-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980114 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.73 49.51 99.1 0.143 0.054 0.998 5 6.9 144327 65.43
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.8 83.7 1.475 0.78 0.517 1 6.2
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 7ASZ 2.73 49.51 136695 7202 98.79 0.20881 0.20646 0.2104 0.25434 0.2537 RANDOM 83.714
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] -4.31 0.44 -0.18 4.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.323 r_dihedral_angle_4_deg 15.025 r_dihedral_angle_3_deg 14.766 r_long_range_B_refined 11.979 r_long_range_B_other 11.979 r_scangle_other 9.17 r_mcangle_it 8.289 r_mcangle_other 8.289 r_dihedral_angle_1_deg 6.055 r_scbond_it 5.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.323 r_dihedral_angle_4_deg 15.025 r_dihedral_angle_3_deg 14.766 r_long_range_B_refined 11.979 r_long_range_B_other 11.979 r_scangle_other 9.17 r_mcangle_it 8.289 r_mcangle_other 8.289 r_dihedral_angle_1_deg 6.055 r_scbond_it 5.855 r_scbond_other 5.854 r_mcbond_it 5.59 r_mcbond_other 5.589 r_angle_refined_deg 1.502 r_angle_other_deg 1.225 r_chiral_restr 0.052 r_gen_planes_other 0.013 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.005 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 44819 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 130
Software Software Software Name Purpose PHENIX refinement REFMAC refinement XDS data reduction XSCALE data scaling PHENIX phasing