☰ Navigation Tabs
Structure of the PTP-like myo-inositol phosphatase from Selenomonas ruminantium in complex with myo-inositol-(1,3,4,5)-tetrakisphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MMJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 293 PEG 8000, sodium chloride, sodium acetate, beta-mercapto ethanol,
Crystal Properties Matthews coefficient Solvent content 3.18 61.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.83 α = 90 b = 138.15 β = 102.3 c = 80.58 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX-300 2011-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97934 CLSI 08ID-1
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 2.1 43.06 100 0.135 5.8 3.8 56995
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 2.1 2.16 100 0.481 2.3 1.8
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 3MMJ 2.1 43.06 55187 1797 99.98 0.15724 0.15666 0.1645 0.17538 0.1847 RANDOM 27.514
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 0.38 -1 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.244 r_dihedral_angle_4_deg 16.148 r_dihedral_angle_3_deg 12.855 r_long_range_B_refined 9.755 r_long_range_B_other 9.713 r_scangle_other 6.652 r_dihedral_angle_1_deg 5.129 r_scbond_it 4.305 r_scbond_other 4.297 r_mcangle_other 3.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.244 r_dihedral_angle_4_deg 16.148 r_dihedral_angle_3_deg 12.855 r_long_range_B_refined 9.755 r_long_range_B_other 9.713 r_scangle_other 6.652 r_dihedral_angle_1_deg 5.129 r_scbond_it 4.305 r_scbond_other 4.297 r_mcangle_other 3.898 r_mcangle_it 3.896 r_mcbond_it 2.68 r_mcbond_other 2.67 r_angle_refined_deg 1.067 r_angle_other_deg 0.586 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5114 Nucleic Acid Atoms Solvent Atoms 663 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing iMOSFLM data reduction