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Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms complexed with cantharidic acid
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-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.12 41.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.535 α = 90 b = 41.518 β = 103.44 c = 97.502 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 4 mirrors 2009-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.93340 ESRF ID14-2
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 1.4 36.47 100 0.078 0.078 60.1 4.6 113739 113739 11.3
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) 1.4 1.48 100 0.347 0.347 13.5 3.2 15375
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 1.4 36.08 98546 98546 9895 100 0.17901 0.17901 0.17649 0.1761 0.20392 0.2032 RANDOM 14.18
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] -0.39 1.04 -0.58 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.642 r_dihedral_angle_4_deg 12.781 r_dihedral_angle_3_deg 11.374 r_dihedral_angle_1_deg 6.18 r_scangle_it 3.291 r_sphericity_free 3.05 r_sphericity_bonded 2.168 r_scbond_it 2.131 r_mcangle_it 1.375 r_angle_refined_deg 1.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.642 r_dihedral_angle_4_deg 12.781 r_dihedral_angle_3_deg 11.374 r_dihedral_angle_1_deg 6.18 r_scangle_it 3.291 r_sphericity_free 3.05 r_sphericity_bonded 2.168 r_scbond_it 2.131 r_mcangle_it 1.375 r_angle_refined_deg 1.308 r_rigid_bond_restr 1.118 r_mcbond_it 0.801 r_chiral_restr 0.091 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 700 Heterogen Atoms 49
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling