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Mode of Action of a Putative Zinc Transporter CzrB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BYR CZRB WITH ZN BOUND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 293 Protein solution 15 mg/ml protein, 20mM Tris, pH 8.0; precipitant solution 0.2M ammonium sulfate, 15% PEG 4000, 0.1M sodium acetate, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.331 α = 90 b = 60.331 β = 90 c = 92.137 γ = 120
Symmetry Space Group P 32 1 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2006-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.7 50 98.9 0.042 54.8 12.8 21179
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 92.4 0.393 4.4 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 CZRB WITH ZN BOUND 1.7 30.71 20053 20053 1086 98.9 0.186 0.1849 0.224 0.2225 RANDOM 28.23
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] -0.41 -0.2 -0.41 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.794 r_dihedral_angle_4_deg 18.097 r_dihedral_angle_3_deg 13.404 r_dihedral_angle_1_deg 4.661 r_scangle_it 4.127 r_scbond_it 2.574 r_mcangle_it 1.299 r_angle_refined_deg 1.202 r_mcbond_it 0.847 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.794 r_dihedral_angle_4_deg 18.097 r_dihedral_angle_3_deg 13.404 r_dihedral_angle_1_deg 4.661 r_scangle_it 4.127 r_scbond_it 2.574 r_mcangle_it 1.299 r_angle_refined_deg 1.202 r_mcbond_it 0.847 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.153 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1310 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing ARP/wARP model building