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Crystal Structure of AtPTP1 at 1.4 angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HNP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1 M sodium citrate (pH 6.0),
25 ~ 30% polyethylene glycol (PEG) 3350, 0.2 M potassium iodide.
Crystal Properties Matthews coefficient Solvent content 2.47 50.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.682 α = 90 b = 42.213 β = 109.49 c = 72.959 γ = 90
Symmetry Space Group C 1 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 PILATUS3 6M 2016-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.978 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.4 50 97.4 0.037 0.04 0.015 0.998 45.3 6.7 65204
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.45 96.6 0.63 0.848 2.8 6.6
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 2HNP 1.4 37.5 61902 3296 97.39 0.13474 0.13309 0.1369 0.16611 0.1688 RANDOM 34.38
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] -2.84 0.01 -0.43 2.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.858 r_scangle_other 15.731 r_long_range_B_other 15.395 r_long_range_B_refined 15.357 r_mcbond_it 14.947 r_mcbond_other 14.938 r_mcangle_other 14.877 r_mcangle_it 14.876 r_scbond_it 14.232 r_scbond_other 14.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.858 r_scangle_other 15.731 r_long_range_B_other 15.395 r_long_range_B_refined 15.357 r_mcbond_it 14.947 r_mcbond_other 14.938 r_mcangle_other 14.877 r_mcangle_it 14.876 r_scbond_it 14.232 r_scbond_other 14.227 r_rigid_bond_restr 14.21 r_dihedral_angle_4_deg 14.192 r_dihedral_angle_3_deg 11.768 r_dihedral_angle_1_deg 5.828 r_angle_refined_deg 1.491 r_angle_other_deg 1.1 r_chiral_restr 0.087 r_gen_planes_refined 0.035 r_gen_planes_other 0.032 r_bond_refined_d 0.011 r_bond_other_d 0.006 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2409 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing