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Crystal structure of an abridged SER TO ALA MUTANT OF THE MATURE ECTODOMAIN of the human receptor-type protein-tyrosine phosphatase ICA512/IA-2 at PH 8.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QT7 PDB ENTRY 2QT7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 30% (W/V) PEG 4000, 0.1 M TrisCl PH 8.5, 0.2 M CACL2, VAPOR DIFFUSION, HANGING DROP, temperature 292
Crystal Properties Matthews coefficient Solvent content 2.05 39.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.554 α = 90 b = 66.544 β = 90 c = 73.712 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 ADSC QUANTUM 270 TOROIDAL FOCUSING MIRROR 2010-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A NSLS X6A
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 1.35 20 98.4 0.039 0.039 44.2 5.6 34457 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37 85.5 0.28 0.28 3 3.1
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 2QT7 1.35 19.45 32636 1735 100 0.17934 0.17694 0.1721 0.22394 0.2216 RANDOM 21.718
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] 1.06 0.09 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.798 r_dihedral_angle_4_deg 26.31 r_dihedral_angle_3_deg 12.466 r_scangle_it 5.807 r_dihedral_angle_1_deg 5.666 r_scbond_it 3.885 r_mcangle_it 2.903 r_mcbond_it 1.84 r_rigid_bond_restr 1.786 r_angle_refined_deg 1.561
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.798 r_dihedral_angle_4_deg 26.31 r_dihedral_angle_3_deg 12.466 r_scangle_it 5.807 r_dihedral_angle_1_deg 5.666 r_scbond_it 3.885 r_mcangle_it 2.903 r_mcbond_it 1.84 r_rigid_bond_restr 1.786 r_angle_refined_deg 1.561 r_chiral_restr 0.107 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1312 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 1
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling