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Crystal structure of the phosphatase domain of human PTP IA-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FH7 PDB entry 2FH7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 294 25% PEG3350, 100 MM BIS-TRIS, 200 MM AMMONIUM ACETATE, PH 6.0, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.23 48.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.907 α = 90 b = 74.229 β = 90 c = 121.067 γ = 90
Symmetry Space Group P 21 21 21
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 2006-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.93971 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.23 50 98.7 0.225 0.191 2.7 6.8 32726 32726
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 2.23 2.34 98.7 0.5 5.9
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 PDB entry 2FH7 2.23 19.73 31493 31493 1035 99.64 0.20123 0.19907 0.2029 0.26698 0.2627 RANDOM 30.077
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] 0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.199 r_dihedral_angle_3_deg 19.892 r_dihedral_angle_4_deg 18.201 r_dihedral_angle_1_deg 11.151 r_scangle_it 9.484 r_scbond_it 6.788 r_mcangle_it 5.526 r_mcbond_it 4.015 r_angle_refined_deg 1.146 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.199 r_dihedral_angle_3_deg 19.892 r_dihedral_angle_4_deg 18.201 r_dihedral_angle_1_deg 11.151 r_scangle_it 9.484 r_scbond_it 6.788 r_mcangle_it 5.526 r_mcbond_it 4.015 r_angle_refined_deg 1.146 r_nbtor_refined 0.3 r_chiral_restr 0.243 r_xyhbond_nbd_refined 0.204 r_symmetry_hbond_refined 0.201 r_nbd_refined 0.165 r_symmetry_vdw_refined 0.153 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4623 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 12
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction CCP4 data scaling