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Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms originally soaked with norcantharidin (which is present in the structure in the hydrolyzed form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S95
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 10mM Tris-HC, 40% MPD, 20% PEG MME 5000 , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.36 47.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.499 α = 90 b = 41.781 β = 96.96 c = 105.905 γ = 90
Symmetry Space Group C 1 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 QUANTUM 315 mirrors 2009-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97550 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.45 40 100 0.063 0.063 200.1 2.6 115060 115060 12.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.45 1.53 100 0.393 0.393 3.9 2.2 15316
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1S95 1.45 37.5 103352 103352 10398 100 0.1643 0.1643 0.16136 0.16 0.19375 0.1926 RANDOM 15.466
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] 0.09 0.96 -0.1 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.952 r_dihedral_angle_3_deg 11.698 r_dihedral_angle_4_deg 9.275 r_dihedral_angle_1_deg 6.212 r_scangle_it 3.558 r_sphericity_free 3.451 r_sphericity_bonded 2.449 r_scbond_it 2.33 r_mcangle_it 1.606 r_angle_refined_deg 1.378
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.952 r_dihedral_angle_3_deg 11.698 r_dihedral_angle_4_deg 9.275 r_dihedral_angle_1_deg 6.212 r_scangle_it 3.558 r_sphericity_free 3.451 r_sphericity_bonded 2.449 r_scbond_it 2.33 r_mcangle_it 1.606 r_angle_refined_deg 1.378 r_rigid_bond_restr 1.321 r_mcbond_it 0.964 r_chiral_restr 0.094 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5056 Nucleic Acid Atoms Solvent Atoms 790 Heterogen Atoms 30
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling