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Crystal structure of human protein tyrosine phosphatase receptor type J
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AHS PDB ENTRY 2AHS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 0.01M NICL2,0.1M TRIS PH 8.5, 1M LI2SO4,150 UL SITTING DROPS
Crystal Properties Matthews coefficient Solvent content 2.16 43.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.06 α = 90 b = 86.06 β = 90 c = 119.54 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 100 CCD MARRESEARCH MIRROS 2006-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 2.5 46.6 98.8 0.06 15.25 3.76 11491 3
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 2.5 2.6 91.2 0.27 4.18 3.13
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 PDB ENTRY 2AHS 2.5 63.25 10857 547 99.7 0.203 0.201 0.2053 0.25 0.2449 RANDOM 29.51
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] 1.23 0.62 1.23 -1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.141 r_dihedral_angle_4_deg 18.465 r_dihedral_angle_3_deg 16.956 r_dihedral_angle_1_deg 6.914 r_scangle_it 1.683 r_angle_refined_deg 1.296 r_scbond_it 1.148 r_angle_other_deg 0.915 r_mcangle_it 0.846 r_mcbond_it 0.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.141 r_dihedral_angle_4_deg 18.465 r_dihedral_angle_3_deg 16.956 r_dihedral_angle_1_deg 6.914 r_scangle_it 1.683 r_angle_refined_deg 1.296 r_scbond_it 1.148 r_angle_other_deg 0.915 r_mcangle_it 0.846 r_mcbond_it 0.485 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.229 r_nbd_other 0.197 r_nbtor_refined 0.19 r_symmetry_vdw_other 0.17 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.155 r_nbtor_other 0.086 r_chiral_restr 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2130 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing