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X ray structure of the periplasmic zinc binding protein ZinT from Salmonella enterica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OEK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 AMMONIUM SULFATE 2 M, SODIUM ACETATE 0.1 M PH 5
Crystal Properties Matthews coefficient Solvent content 3.41 63.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.534 α = 90 b = 58.534 β = 90 c = 289.316 γ = 120
Symmetry Space Group P 61 2 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 MARMOSAIC 225 mm CCD 2010-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 50 99.1 0.11 25.62 12.7 14007
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 99.9 0.24 14.75 14.3
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 PDB ENTRY 10EK 2.3 50.69 13233 693 99.26 0.22388 0.22054 0.2138 0.28841 0.279 RANDOM 23.858
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] -0.05 -0.03 -0.05 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.358 r_dihedral_angle_3_deg 17.537 r_dihedral_angle_4_deg 14.068 r_dihedral_angle_1_deg 5.547 r_scangle_it 3.365 r_scbond_it 1.993 r_mcangle_it 1.457 r_angle_refined_deg 1.283 r_mcbond_it 0.756 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.358 r_dihedral_angle_3_deg 17.537 r_dihedral_angle_4_deg 14.068 r_dihedral_angle_1_deg 5.547 r_scangle_it 3.365 r_scbond_it 1.993 r_mcangle_it 1.457 r_angle_refined_deg 1.283 r_mcbond_it 0.756 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1503 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing