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Structure of Y68F mutant Mn-Bound 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 4.6 277.15 0.1M SODIUM ACETATE TRIHYDRATE pH 4.6, 2M AMMONIUM SULPHATE
Crystal Properties Matthews coefficient Solvent content 3.9 68.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.952 α = 90 b = 93.952 β = 90 c = 94.567 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 2015-07-31 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 1.84 40.8 99.9 23.5 6.4 45940 25.3
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 1.84 1.87 100 2.1 6.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4UDN 1.84 40.8 40046 2040 99.48 0.14248 0.14009 0.18905 0.1731 RANDOM 35.228
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] 0.01 0.01 0.01 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.729 r_sphericity_free 34.136 r_sphericity_bonded 18.119 r_dihedral_angle_4_deg 15.375 r_dihedral_angle_3_deg 14.832 r_dihedral_angle_1_deg 6.379 r_long_range_B_refined 6.307 r_scbond_it 5.449 r_mcangle_it 4.067 r_mcbond_it 3.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.729 r_sphericity_free 34.136 r_sphericity_bonded 18.119 r_dihedral_angle_4_deg 15.375 r_dihedral_angle_3_deg 14.832 r_dihedral_angle_1_deg 6.379 r_long_range_B_refined 6.307 r_scbond_it 5.449 r_mcangle_it 4.067 r_mcbond_it 3.747 r_rigid_bond_restr 3.545 r_angle_refined_deg 1.858 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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_it r_scangle_other r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2082 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing