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Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c)with two Mn2+ atoms
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, MPD 40%, PEG MME 5000 20%, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.35 47.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.414 α = 90 b = 41.755 β = 97.07 c = 105.432 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 2008-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.89225 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 2 65.8 100 0.099 0.099 14.8 6.6 44744 44744 21.3
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) 2 2.11 100 0.285 0.285 5.7 5.8 5698
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 2 65.8 40681 40681 4062 100 0.16653 0.16653 0.16129 0.1604 0.21859 0.2187 RANDOM 24.09
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] 0.12 2.12 -0.61 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.922 r_dihedral_angle_3_deg 15.902 r_dihedral_angle_4_deg 15.606 r_dihedral_angle_1_deg 6.634 r_scangle_it 5.66 r_scbond_it 3.474 r_mcangle_it 2.044 r_angle_refined_deg 1.83 r_mcbond_it 1.189 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.922 r_dihedral_angle_3_deg 15.902 r_dihedral_angle_4_deg 15.606 r_dihedral_angle_1_deg 6.634 r_scangle_it 5.66 r_scbond_it 3.474 r_mcangle_it 2.044 r_angle_refined_deg 1.83 r_mcbond_it 1.189 r_chiral_restr 0.129 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5056 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 4
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling