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Crystal structure of Tk-PTP in the G95A mutant form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Z5A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Bis-Tris (pH 6.25) and 0.8M magnesium formate dehydrate
Crystal Properties Matthews coefficient Solvent content 3.13 60.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.796 α = 90 b = 154.796 β = 90 c = 75.24 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC QUANTUM 270 2017-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.000 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.298 77.4 95.2 27 4.3 28515
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.298 2.34
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 5Z5A 2.3 77.4 25754 1374 90.58 0.2216 0.21923 0.226 0.26459 0.264 RANDOM 37.539
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] -0.16 -0.08 -0.16 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.99 r_dihedral_angle_3_deg 18.449 r_dihedral_angle_4_deg 17.165 r_dihedral_angle_1_deg 7.384 r_long_range_B_refined 6.952 r_long_range_B_other 6.951 r_scangle_other 5.22 r_mcangle_it 4.445 r_mcangle_other 4.444 r_scbond_it 3.267
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.99 r_dihedral_angle_3_deg 18.449 r_dihedral_angle_4_deg 17.165 r_dihedral_angle_1_deg 7.384 r_long_range_B_refined 6.952 r_long_range_B_other 6.951 r_scangle_other 5.22 r_mcangle_it 4.445 r_mcangle_other 4.444 r_scbond_it 3.267 r_scbond_other 3.267 r_mcbond_it 2.85 r_mcbond_other 2.85 r_angle_refined_deg 1.868 r_angle_other_deg 1.077 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3707 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing