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Crystal Structure of the catalytic domain of PTP10D from Drosophila melanogaster with a small molecule inhibitor Vanadate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S3E PDB ID 3S3E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 15% PEG 4000, 120mM Citrate, 10% iso-propanol, 10% n-Butanol, 10% 1,4-Butanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.7 66.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.07 α = 90 b = 103.07 β = 90 c = 173.401 γ = 120
Symmetry Space Group P 31 2 1
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 bent collimating mirror and toroid 2010-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.00 ESRF BM14
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 2.7 45 100 0.113 11.9 5.8 29943 -5 44.99
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 2.7 2.85 100 0.435 3.7 5.8 25051
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 (All) 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 ID 3S3E 2.7 39.68 28357 28357 1514 99.8 0.23982 0.23982 0.23813 0.2086 0.27177 0.2425 RANDOM 38.07
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] 0.12 0.06 0.12 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.811 r_dihedral_angle_4_deg 18.134 r_dihedral_angle_3_deg 17.82 r_dihedral_angle_1_deg 6.885 r_scangle_it 2.062 r_scbond_it 1.264 r_angle_refined_deg 1.261 r_mcangle_it 0.711 r_mcbond_it 0.357 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.811 r_dihedral_angle_4_deg 18.134 r_dihedral_angle_3_deg 17.82 r_dihedral_angle_1_deg 6.885 r_scangle_it 2.062 r_scbond_it 1.264 r_angle_refined_deg 1.261 r_mcangle_it 0.711 r_mcbond_it 0.357 r_chiral_restr 0.101 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4684 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 29
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling