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Crystal structure of bacterial serine phosphatase with His-tag mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F1M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.2 M MgCl2, 0.1 M Tris-HCl (pH=8.0), 30% PEG 4000.
Crystal Properties Matthews coefficient Solvent content 2.16 43.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.793 α = 90 b = 86.355 β = 90 c = 38.896 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2016-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9735 SSRF BL18U1
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 1.4 30 99.3 0.062 44.8 5.4 52150
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 1.4 1.45 0.557
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 5F1M 1.4 30 49487 2610 99.1 0.13204 0.13013 0.1467 0.16792 0.1817 RANDOM 22.469
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 -0.62 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.894 r_dihedral_angle_4_deg 20.128 r_sphericity_free 17.939 r_dihedral_angle_3_deg 13.865 r_sphericity_bonded 11.012 r_dihedral_angle_1_deg 6.936 r_rigid_bond_restr 6.028 r_scangle_other 4.904 r_scbond_other 4.537 r_scbond_it 4.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.894 r_dihedral_angle_4_deg 20.128 r_sphericity_free 17.939 r_dihedral_angle_3_deg 13.865 r_sphericity_bonded 11.012 r_dihedral_angle_1_deg 6.936 r_rigid_bond_restr 6.028 r_scangle_other 4.904 r_scbond_other 4.537 r_scbond_it 4.535 r_long_range_B_refined 3.866 r_long_range_B_other 3.866 r_angle_refined_deg 2.587 r_mcangle_other 2.342 r_mcangle_it 2.334 r_mcbond_it 2.125 r_mcbond_other 2.089 r_angle_other_deg 1.27 r_chiral_restr 0.207 r_bond_refined_d 0.031 r_gen_planes_refined 0.013 r_bond_other_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2024 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing