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Crystal structure of the catalytic domain of serine threonine protein phosphatase PstP in complex with 2 Manganese ions.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TXO PDB ENTRY 1TXO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 14% PEG 8000, 50MM KH2PO4 PH6.5, 15% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.142 α = 90 b = 69.142 β = 90 c = 89.431 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 ADSC CCD MIRRORS 2005-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2 60 92.8 0.09 11.67 3.5 15969 3.96
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 2 2.2 84.1 0.4 3.96 3.5
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 1TXO 2 59.87 15173 799 93 0.199 0.197 0.1985 0.243 0.2424 RANDOM 25.87
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] 0.6 0.3 0.6 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.566 r_dihedral_angle_4_deg 21.521 r_dihedral_angle_3_deg 15.724 r_dihedral_angle_1_deg 7.431 r_scangle_it 4.408 r_scbond_it 2.731 r_mcangle_it 1.841 r_angle_refined_deg 1.75 r_mcbond_it 1.151 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.566 r_dihedral_angle_4_deg 21.521 r_dihedral_angle_3_deg 15.724 r_dihedral_angle_1_deg 7.431 r_scangle_it 4.408 r_scbond_it 2.731 r_mcangle_it 1.841 r_angle_refined_deg 1.75 r_mcbond_it 1.151 r_nbtor_refined 0.305 r_nbd_refined 0.237 r_symmetry_vdw_refined 0.226 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.103 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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_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 1667 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing