☰ Navigation Tabs
The Crystal Structure of PTP1B from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7FRR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M MgCl2, 0.1M Bis-Tris pH6.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.1 60.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.148 α = 90 b = 88.148 β = 90 c = 103.396 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS PILATUS 6M 2023-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
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 1.55 44.07 99.9 0.089 15 8.7 67746
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 1.55 1.58 1.013
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.55 44.07 67702 3409 99.876 0.16 0.1591 0.1725 0.1841 0.1981 18.053
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] 0.043 0.021 0.043 -0.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.073 r_dihedral_angle_3_deg 12.804 r_lrange_it 6.833 r_lrange_other 6.548 r_dihedral_angle_1_deg 5.936 r_dihedral_angle_2_deg 5.361 r_scangle_it 4.673 r_scangle_other 4.672 r_scbond_it 2.9 r_scbond_other 2.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.073 r_dihedral_angle_3_deg 12.804 r_lrange_it 6.833 r_lrange_other 6.548 r_dihedral_angle_1_deg 5.936 r_dihedral_angle_2_deg 5.361 r_scangle_it 4.673 r_scangle_other 4.672 r_scbond_it 2.9 r_scbond_other 2.899 r_mcangle_other 2.635 r_mcangle_it 2.631 r_mcbond_it 1.671 r_mcbond_other 1.663 r_angle_refined_deg 1.436 r_angle_other_deg 0.506 r_metal_ion_refined 0.475 r_symmetry_xyhbond_nbd_refined 0.225 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.186 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.181 r_nbd_other 0.143 r_symmetry_nbd_refined 0.14 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_symmetry_xyhbond_nbd_other 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2446 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing