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Metal-bound C-terminal domain of CzcD transporter from Thermotoga maritima
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZZT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.6 M-2.0 M ammonium sulfate, 1.0 mM ZnSO4
Crystal Properties Matthews coefficient Solvent content 3.22 61.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.42 α = 90 b = 97.42 β = 90 c = 84.06 γ = 120
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 16M 2016-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 2.4 49 100 0.992 12.1 5.1 6149
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 2.4 2.49 0.727
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 2ZZT 2.4 48.76 5289 618 96.25 0.23902 0.2339 0.241 0.28352 0.2853 RANDOM 81.706
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] 0.24 0.12 0.24 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.843 r_dihedral_angle_4_deg 15.212 r_dihedral_angle_3_deg 15.002 r_dihedral_angle_1_deg 6.057 r_long_range_B_other 5.87 r_long_range_B_refined 5.858 r_scangle_other 3.745 r_mcangle_it 3.605 r_mcangle_other 3.601 r_mcbond_it 2.408
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.843 r_dihedral_angle_4_deg 15.212 r_dihedral_angle_3_deg 15.002 r_dihedral_angle_1_deg 6.057 r_long_range_B_other 5.87 r_long_range_B_refined 5.858 r_scangle_other 3.745 r_mcangle_it 3.605 r_mcangle_other 3.601 r_mcbond_it 2.408 r_mcbond_other 2.405 r_scbond_it 2.323 r_scbond_other 2.311 r_angle_refined_deg 1.236 r_angle_other_deg 1.122 r_chiral_restr 0.041 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 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 689 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 11
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement