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Crystal structure of the human protein tyrosine phosphatase, non- receptor type 4, PDZ domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OCS PDB ENTRIES 2OCS, 2HE2, 1QAV experimental model PDB 2HE2 PDB ENTRIES 2OCS, 2HE2, 1QAV experimental model PDB 1QAV PDB ENTRIES 2OCS, 2HE2, 1QAV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 20% PEG 3350, 0.20M (NH4)2H(CIT), PH 5
Crystal Properties Matthews coefficient Solvent content 2.09 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.489 α = 90 b = 71.015 β = 90 c = 71.598 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 2008-01-26 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 1.9 50 100 0.1 10.9 7 15306 2.8 30.5
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 1.9 2 100 0.59 2.8 6.4
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 ENTRIES 2OCS, 2HE2, 1QAV 1.9 45 14492 765 100 0.21 0.208 0.2111 0.243 0.2411 RANDOM 27.32
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] 1.56 -0.9 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.526 r_dihedral_angle_4_deg 20.304 r_dihedral_angle_3_deg 11.308 r_scangle_it 8.366 r_dihedral_angle_1_deg 6.414 r_scbond_it 5.889 r_mcangle_it 4.235 r_mcbond_it 2.861 r_angle_refined_deg 1.448 r_angle_other_deg 0.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.526 r_dihedral_angle_4_deg 20.304 r_dihedral_angle_3_deg 11.308 r_scangle_it 8.366 r_dihedral_angle_1_deg 6.414 r_scbond_it 5.889 r_mcangle_it 4.235 r_mcbond_it 2.861 r_angle_refined_deg 1.448 r_angle_other_deg 0.921 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.001 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_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 1424 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing