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Crystal Structure of AtPTP1 at 1.7 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 2.12 41.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.536 α = 90 b = 38.97 β = 110.815 c = 75.525 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 PILATUS 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 1.7 50 96.6 0.043 0.049 0.021 0.994 30.4 4.8 34099
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 78.4 0.191 0.22 0.106 0.951 6 4
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2HNP 1.7 37.201 34081 1713 96.465 0.152 0.1511 0.1743 0.1958 Random selection 16.394
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] 0.138 0.088 -0.251 0.035
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.11 r_dihedral_angle_4_deg 13.933 r_dihedral_angle_3_deg 11.811 r_lrange_it 6.357 r_lrange_other 6.271 r_dihedral_angle_1_deg 6.105 r_scangle_it 5.041 r_scangle_other 5.04 r_mcangle_other 3.556 r_mcangle_it 3.554
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.11 r_dihedral_angle_4_deg 13.933 r_dihedral_angle_3_deg 11.811 r_lrange_it 6.357 r_lrange_other 6.271 r_dihedral_angle_1_deg 6.105 r_scangle_it 5.041 r_scangle_other 5.04 r_mcangle_other 3.556 r_mcangle_it 3.554 r_scbond_it 3.292 r_scbond_other 3.29 r_mcbond_it 2.334 r_mcbond_other 2.328 r_angle_refined_deg 1.279 r_angle_other_deg 0.339 r_nbd_refined 0.211 r_nbtor_refined 0.167 r_nbd_other 0.166 r_symmetry_nbd_other 0.163 r_symmetry_xyhbond_nbd_refined 0.154 r_xyhbond_nbd_refined 0.149 r_symmetry_nbd_refined 0.136 r_symmetry_xyhbond_nbd_other 0.107 r_symmetry_nbtor_other 0.091 r_xyhbond_nbd_other 0.087 r_chiral_restr 0.057 r_gen_planes_refined 0.056 r_gen_planes_other 0.052 r_bond_refined_d 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2391 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing