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Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with TrkC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YD4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.5 10% w/v PEG MME 5k, 0.1 M HEPES pH 7, 5% w/v Tacsimate
Crystal Properties Matthews coefficient Solvent content 3.71 66.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.42 α = 73.37 b = 93.12 β = 89.45 c = 99.38 γ = 74.23
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-F 2013-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 3.05 81.02 96.3 0.069 8.8 1.8 51063
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 3.05 3.13 96.6 0.347 1.5 1.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2YD4 3.05 94.96 48530 2533 96.23 0.22682 0.2261 0.23994 0.2231 RANDOM 115.246
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] -5.06 2.72 2.24 0.86 -5.08 1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.552 r_dihedral_angle_3_deg 14.676 r_dihedral_angle_4_deg 12.754 r_dihedral_angle_1_deg 5.68 r_long_range_B_refined 5.663 r_long_range_B_other 5.663 r_scangle_other 3.773 r_mcangle_it 3.206 r_mcangle_other 3.206 r_scbond_it 2.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.552 r_dihedral_angle_3_deg 14.676 r_dihedral_angle_4_deg 12.754 r_dihedral_angle_1_deg 5.68 r_long_range_B_refined 5.663 r_long_range_B_other 5.663 r_scangle_other 3.773 r_mcangle_it 3.206 r_mcangle_other 3.206 r_scbond_it 2.231 r_scbond_other 2.23 r_mcbond_it 1.913 r_mcbond_other 1.913 r_angle_refined_deg 1.045 r_angle_other_deg 0.769 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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 10630 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing