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Structure of Y68F mutant metal free periplasmic metal binding protein from candidatus liberibacter asiaticus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277.15 0.1M SODIUM ACETATE TRIHYDRATE PH 4.6, 2M AMMONIUM SULPHATE
Crystal Properties Matthews coefficient Solvent content 3.91 68.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.23 α = 90 b = 94.23 β = 90 c = 94.31 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 100 CCD MARRESEARCH 2015-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.79 81.61 97.6 10.1 5.8 44757 20.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.89 84 2.4 5.4
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 4UDN 1.8 81.61 42469 2256 99.17 0.17186 0.17049 0.1832 0.19735 0.2058 RANDOM 29.627
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] 0.2 0.1 0.2 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.368 r_dihedral_angle_4_deg 18.732 r_dihedral_angle_3_deg 13.294 r_long_range_B_refined 6.719 r_long_range_B_other 6.718 r_dihedral_angle_1_deg 6.247 r_scangle_other 2.479 r_mcangle_other 2.141 r_mcangle_it 2.138 r_angle_refined_deg 1.656
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.368 r_dihedral_angle_4_deg 18.732 r_dihedral_angle_3_deg 13.294 r_long_range_B_refined 6.719 r_long_range_B_other 6.718 r_dihedral_angle_1_deg 6.247 r_scangle_other 2.479 r_mcangle_other 2.141 r_mcangle_it 2.138 r_angle_refined_deg 1.656 r_scbond_it 1.515 r_scbond_other 1.515 r_mcbond_it 1.266 r_mcbond_other 1.201 r_angle_other_deg 1.016 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2120 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing