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Crystal structure of the receptor protein tyrosine phosphatase mu ectodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C9A PDB ENTRY 2C9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 100MM BIS-TRIS-PROPANE, PH 6.5 22.5% (W/V) PEG-SMEAR, 200MM K-THIOCYANATE
Crystal Properties Matthews coefficient Solvent content 3.07 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.336 α = 90 b = 69.325 β = 113.52 c = 97.487 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 CCD ADSC CCD 2005-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 3.1 20 98.6 0.16 10.3 5.3 19030
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 3.1 3.2 89 0.61 2.5 4.6
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 PDB ENTRY 2C9A 3.1 20 17792 969 100 0.246 0.242 0.2445 0.32 0.312 RANDOM 27.1
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] -5.03 -1.94 5.12 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.455 r_dihedral_angle_3_deg 19.584 r_dihedral_angle_4_deg 16.173 r_dihedral_angle_1_deg 7.602 r_angle_refined_deg 1.243 r_mcangle_it 0.858 r_angle_other_deg 0.836 r_scangle_it 0.752 r_mcbond_it 0.481 r_scbond_it 0.378
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.455 r_dihedral_angle_3_deg 19.584 r_dihedral_angle_4_deg 16.173 r_dihedral_angle_1_deg 7.602 r_angle_refined_deg 1.243 r_mcangle_it 0.858 r_angle_other_deg 0.836 r_scangle_it 0.752 r_mcbond_it 0.481 r_scbond_it 0.378 r_symmetry_vdw_other 0.223 r_nbd_refined 0.187 r_nbd_other 0.187 r_nbtor_refined 0.181 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.154 r_symmetry_hbond_refined 0.134 r_nbtor_other 0.087 r_chiral_restr 0.074 r_mcbond_other 0.041 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_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 4423 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 100
Software Software Software Name Purpose HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing PHASER phasing REFMAC refinement