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Crystal structure of human protein tyrosine phosphatase kappa at 1.95A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RPM PDB ENTRY 1RPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP SITTING DROP, 0.2M NANO3, 20% PEG3350, 10% ETHYLENE GLYCOL
Crystal Properties Matthews coefficient Solvent content 3.2 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.373 α = 90 b = 91.373 β = 90 c = 108.415 γ = 90
Symmetry Space Group P 43 21 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 MARRESEARCH MIRRORS 2005-11-19 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 1.95 52 96.3 0.08 11.14 6.1 32866 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 1.95 2.05 87.7 0.29 4.1 5.1
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 1RPM 1.95 69.84 31191 1635 96.3 0.201 0.2 0.2017 0.218 0.2197 RANDOM 31.75
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] 0.59 0.59 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.479 r_dihedral_angle_4_deg 16.465 r_dihedral_angle_3_deg 13.931 r_dihedral_angle_1_deg 6.255 r_scangle_it 2.042 r_scbond_it 1.397 r_angle_refined_deg 1.202 r_mcangle_it 0.997 r_angle_other_deg 0.864 r_mcbond_it 0.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.479 r_dihedral_angle_4_deg 16.465 r_dihedral_angle_3_deg 13.931 r_dihedral_angle_1_deg 6.255 r_scangle_it 2.042 r_scbond_it 1.397 r_angle_refined_deg 1.202 r_mcangle_it 0.997 r_angle_other_deg 0.864 r_mcbond_it 0.624 r_symmetry_vdw_other 0.29 r_nbd_other 0.192 r_nbd_refined 0.189 r_nbtor_refined 0.179 r_symmetry_vdw_refined 0.17 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.142 r_nbtor_other 0.082 r_chiral_restr 0.069 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 2299 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing