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structure of periplasmic metal binding protein from candidatus liberibacter asiaticus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HH8 PDB ENTRY 3HH8
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 3.9 68.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.06 α = 90 b = 94.06 β = 90 c = 94.51 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 2013-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER
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 1.63 30.85 95.7 0.07 18.5 8 57802 2 21.9
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 1.63 1.72 92.1 0.92 2.1 6.7
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 3HH8 1.63 29.29 54875 2927 95.34 0.1683 0.16694 0.178 0.19419 0.2006 RANDOM 26.332
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] 0.09 0.09 0.09 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.314 r_dihedral_angle_4_deg 18.17 r_dihedral_angle_3_deg 12.827 r_dihedral_angle_1_deg 6.736 r_scbond_it 4.726 r_mcangle_it 3.593 r_mcbond_it 2.75 r_mcbond_other 2.553 r_angle_refined_deg 1.797 r_angle_other_deg 0.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.314 r_dihedral_angle_4_deg 18.17 r_dihedral_angle_3_deg 12.827 r_dihedral_angle_1_deg 6.736 r_scbond_it 4.726 r_mcangle_it 3.593 r_mcbond_it 2.75 r_mcbond_other 2.553 r_angle_refined_deg 1.797 r_angle_other_deg 0.896 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.003 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 2089 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing