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PorX with Zn (primitive orthorhombic crystal form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8TED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.16 M calcium acetate, 0.08 M sodium cacodylate pH 6.5, 14.4% polyethylene glycol 8000, 25% glycerol and 0.2 mM Zinc chloride
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.868 α = 90 b = 97.058 β = 90 c = 132.037 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 EIGER X 9M 2022-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.283 CLSI 08ID-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 2.72 50 99.8 0.113 0.118 0.033 0.998 5.4 12.7 31924
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 2.72 2.77 97.7 0.829 0.87 0.257 0.901 10.5
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 2.72 48.58 30273 1593 98 0.20717 0.20431 0.208 0.26111 0.2543 RANDOM 74.039
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] 3.65 0.67 -4.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.902 r_long_range_B_refined 10.191 r_long_range_B_other 10.191 r_dihedral_angle_2_deg 9.563 r_dihedral_angle_1_deg 7.11 r_scangle_other 6.043 r_mcangle_it 5.447 r_mcangle_other 5.447 r_scbond_it 3.715 r_scbond_other 3.715
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.902 r_long_range_B_refined 10.191 r_long_range_B_other 10.191 r_dihedral_angle_2_deg 9.563 r_dihedral_angle_1_deg 7.11 r_scangle_other 6.043 r_mcangle_it 5.447 r_mcangle_other 5.447 r_scbond_it 3.715 r_scbond_other 3.715 r_mcbond_it 3.457 r_mcbond_other 3.457 r_angle_refined_deg 1.329 r_angle_other_deg 0.438 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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 8273 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing