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Crystal Structure of the Catalytic Domain of Human Tyrosine Receptor Phosphatase Beta
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RPM 1RPM.PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 277 PEG6000, Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.9 57.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.368 α = 90 b = 123.368 β = 90 c = 179.569 γ = 120
Symmetry Space Group P 61 2 2
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 MARMOSAIC 225 mm CCD 2005-07-04 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) 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 2.1 53.4 99.2 47341
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 95.1
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 (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 1RPM.PDB 2.1 53.4 44882 44882 2394 99.2 0.155 0.152 0.1979 0.206 0.1957 RANDOM 23.14
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] -0.19 -0.09 -0.19 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.211 r_dihedral_angle_3_deg 13.223 r_dihedral_angle_4_deg 13.063 r_scangle_it 11.135 r_scbond_it 9.518 r_mcangle_it 6.752 r_dihedral_angle_1_deg 6.312 r_mcbond_it 5.038 r_mcbond_other 2.003 r_angle_refined_deg 1.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.211 r_dihedral_angle_3_deg 13.223 r_dihedral_angle_4_deg 13.063 r_scangle_it 11.135 r_scbond_it 9.518 r_mcangle_it 6.752 r_dihedral_angle_1_deg 6.312 r_mcbond_it 5.038 r_mcbond_other 2.003 r_angle_refined_deg 1.337 r_angle_other_deg 0.895 r_symmetry_hbond_refined 0.467 r_symmetry_vdw_refined 0.295 r_symmetry_vdw_other 0.288 r_xyhbond_nbd_refined 0.219 r_nbd_refined 0.202 r_nbd_other 0.186 r_nbtor_refined 0.173 r_chiral_restr 0.121 r_nbtor_other 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4444 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing