☰ Navigation Tabs
Structure of zinc-bound ZrgA deletion 124-184 from Vibrio cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8EZW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 4.6 296 Protein at 10 mg/mL was combined in a 1:1 ratio with precipitant solution containing 0.1 M sodium acetate pH 4.6, 0.2 M ammonium acetate, 27% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.18 43.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.991 α = 90 b = 66.914 β = 99.92 c = 88.242 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 PILATUS3 6M 2022-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00 ALS 5.0.2
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 2.41 46.67 99.4 0.996 9.3 3.8 36368
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 2.41 2.5 99.8 0.8 3.9
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 8EZW 2.41 46.67 34622 1734 99.24 0.22012 0.21802 0.2251 0.26196 0.264 RANDOM 40.53
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] -2.64 -3.6 -0.11 3.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.958 r_dihedral_angle_4_deg 20.32 r_dihedral_angle_3_deg 18.124 r_long_range_B_refined 9.271 r_long_range_B_other 9.27 r_dihedral_angle_1_deg 7.04 r_scangle_other 5.485 r_mcangle_other 4.718 r_mcangle_it 4.716 r_scbond_it 3.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.958 r_dihedral_angle_4_deg 20.32 r_dihedral_angle_3_deg 18.124 r_long_range_B_refined 9.271 r_long_range_B_other 9.27 r_dihedral_angle_1_deg 7.04 r_scangle_other 5.485 r_mcangle_other 4.718 r_mcangle_it 4.716 r_scbond_it 3.372 r_scbond_other 3.37 r_mcbond_it 2.951 r_mcbond_other 2.945 r_angle_other_deg 1.362 r_angle_refined_deg 1.323 r_chiral_restr 0.06 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 6660 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing