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Crystal Structure of the Human Receptor Phosphatase PTPRT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RPM PDB entries 1RPM, 2C7S, 1LAR, 2FH7 experimental model PDB 2C7S PDB entries 1RPM, 2C7S, 1LAR, 2FH7 experimental model PDB 1LAR PDB entries 1RPM, 2C7S, 1LAR, 2FH7 experimental model PDB 2FH7 PDB entries 1RPM, 2C7S, 1LAR, 2FH7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2M LiCl, 0.1M HEPES, 20.0% PEG 6000, 10.0% Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.186 α = 90 b = 86.697 β = 99.89 c = 91.12 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU RAXIS HTC 2007-01-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54180
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 89.77 100 0.092 0.092 16 3.7 52802 18.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 100 0.595 0.595 2.6 3.6
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 (All) 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 PDB entries 1RPM, 2C7S, 1LAR, 2FH7 1.8 89.77 50081 50081 2688 99.92 0.14709 0.14709 0.14488 0.1552 0.18758 0.1959 RANDOM 22.417
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] 0.09 -0.35 0.3 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.446 r_dihedral_angle_4_deg 18.286 r_dihedral_angle_3_deg 12.178 r_scangle_it 8.471 r_scbond_it 7.122 r_dihedral_angle_1_deg 6.4 r_mcangle_it 4.816 r_mcbond_it 3.651 r_mcbond_other 1.839 r_angle_refined_deg 1.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.446 r_dihedral_angle_4_deg 18.286 r_dihedral_angle_3_deg 12.178 r_scangle_it 8.471 r_scbond_it 7.122 r_dihedral_angle_1_deg 6.4 r_mcangle_it 4.816 r_mcbond_it 3.651 r_mcbond_other 1.839 r_angle_refined_deg 1.453 r_angle_other_deg 0.909 r_symmetry_vdw_other 0.26 r_nbd_refined 0.217 r_nbd_other 0.202 r_nbtor_refined 0.182 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.162 r_symmetry_vdw_refined 0.093 r_chiral_restr 0.089 r_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4421 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction CCP4 data scaling PHASER phasing