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The structure of phosphotyrosine phosphatase 1B in complex with compound 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PTY PDB ENTRY 1PTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 284 PEG 3350, MGCL2, HEPES, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 284K
Crystal Properties Matthews coefficient Solvent content 3.59 65.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.431 α = 90 b = 86.621 β = 90 c = 139.193 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH 2000-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 21 99.6 0.064 12.3 6.83 61693 61477 -3 -3 37.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 100 0.439 1.4 7.24 10142
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1PTY 2.1 15 61478 56198 3007 96.29 0.19284 0.19152 0.189 0.21676 0.2156 RANDOM 45.576
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] 0.2 -1.65 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.619 r_dihedral_angle_4_deg 21.494 r_dihedral_angle_3_deg 16.179 r_dihedral_angle_1_deg 5.496 r_scangle_it 2.159 r_scbond_it 1.41 r_angle_refined_deg 1.254 r_mcangle_it 1.007 r_mcbond_it 0.612 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.619 r_dihedral_angle_4_deg 21.494 r_dihedral_angle_3_deg 16.179 r_dihedral_angle_1_deg 5.496 r_scangle_it 2.159 r_scbond_it 1.41 r_angle_refined_deg 1.254 r_mcangle_it 1.007 r_mcbond_it 0.612 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.191 r_nbd_refined 0.189 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.151 r_chiral_restr 0.084 r_symmetry_metal_ion_refined 0.04 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other 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 4638 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement X-GEN data reduction CNX refinement X-GEN data scaling CNX phasing