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Structure of the PTP-like myo-inositol phosphatase from Selenomonas ruminantium in complex with myo-inositol-(1,4,5)-trikisphosphate
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 acetate, sodium chloride, beta-mercapto ethanol
Crystal Properties Matthews coefficient Solvent content 3.16 61.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.98 α = 90 b = 137.67 β = 102.42 c = 80.01 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 .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 44.9 99.9 0.128 5.2 3.3 65377
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 2.15 2.22 100 0.523 1.9 3.3
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 2.15 44.89 50511 2154 99.86 0.19768 0.19677 0.1886 0.21947 0.2063 RANDOM 31.039
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] -2.59 0.48 -0.82 2.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.71 r_dihedral_angle_4_deg 18.685 r_dihedral_angle_3_deg 13.2 r_long_range_B_refined 9.339 r_long_range_B_other 9.326 r_scangle_other 6.292 r_dihedral_angle_1_deg 5.192 r_mcangle_other 4.501 r_mcangle_it 4.5 r_scbond_it 4.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.71 r_dihedral_angle_4_deg 18.685 r_dihedral_angle_3_deg 13.2 r_long_range_B_refined 9.339 r_long_range_B_other 9.326 r_scangle_other 6.292 r_dihedral_angle_1_deg 5.192 r_mcangle_other 4.501 r_mcangle_it 4.5 r_scbond_it 4.112 r_scbond_other 4.112 r_mcbond_it 3.027 r_mcbond_other 3.023 r_angle_refined_deg 1.153 r_angle_other_deg 0.62 r_chiral_restr 0.059 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 5096 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling