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structure of Zn-bound periplasmic metal binding protein from candidatus liberibacter asiaticus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CL2 PDB ENTRY 4CL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 0.1M SODIUM ACETATE TRIHYDRATE PH 4.6, 2M AMMONIUM SULPHATE
Crystal Properties Matthews coefficient Solvent content 4.05 69.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.37 α = 90 b = 94.37 β = 90 c = 94.43 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 IMAGE PLATE MAR scanner 345 mm plate MIRROR 2014-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 2.21 47.22 98.9 0.05 37.2 11.5 24473 2
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 2.21 2.33 92.5 0.16 15.6 10.4
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 4CL2 2.22 42.24 23203 1243 99.82 0.15447 0.15305 0.1607 0.18142 0.186 RANDOM 23.554
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] 0.16 0.16 0.16 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.614 r_dihedral_angle_4_deg 16.116 r_dihedral_angle_3_deg 13.625 r_dihedral_angle_1_deg 5.73 r_scbond_it 4.912 r_mcangle_it 4.409 r_mcbond_it 3.219 r_mcbond_other 3.102 r_angle_refined_deg 1.083 r_angle_other_deg 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.614 r_dihedral_angle_4_deg 16.116 r_dihedral_angle_3_deg 13.625 r_dihedral_angle_1_deg 5.73 r_scbond_it 4.912 r_mcangle_it 4.409 r_mcbond_it 3.219 r_mcbond_other 3.102 r_angle_refined_deg 1.083 r_angle_other_deg 0.73 r_chiral_restr 0.068 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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_mcangle_other r_scbond_other r_scangle_it 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 2105 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing