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structure of S38A 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 3.98 69.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.07 α = 90 b = 94.07 β = 90 c = 94.68 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 2015-10-12 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 1.86 81.48 97.9 10.2 5.8 40167
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 1.86 1.96 85.6 2.3 5.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4UDN 1.87 81.47 38248 1885 99.5 0.15953 0.15797 0.19151 0.1844 RANDOM 30.143
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] 0.07 0.03 0.07 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.489 r_dihedral_angle_4_deg 18.164 r_dihedral_angle_3_deg 13.352 r_long_range_B_refined 10.347 r_long_range_B_other 10.346 r_dihedral_angle_1_deg 6.986 r_scangle_other 6.963 r_scbond_it 4.865 r_scbond_other 4.864 r_mcangle_other 4.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.489 r_dihedral_angle_4_deg 18.164 r_dihedral_angle_3_deg 13.352 r_long_range_B_refined 10.347 r_long_range_B_other 10.346 r_dihedral_angle_1_deg 6.986 r_scangle_other 6.963 r_scbond_it 4.865 r_scbond_other 4.864 r_mcangle_other 4.225 r_mcangle_it 4.206 r_mcbond_it 3.151 r_mcbond_other 2.686 r_angle_refined_deg 1.904 r_angle_other_deg 1.066 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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 2133 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing