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Crystal structure of the 2H-phosphatase domain of Sts-2 in complex with tungstate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D4I PDB entry 3d4i
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.2 M Lithium sulfate, 0.1 M Tris-HCl, 5-20 mM Strontium chloride, 20% PEG8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.205 α = 90 b = 116.665 β = 90 c = 121.471 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 210 monochromator 2006-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.0 NSLS X6A
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 2.25 100 99.4 0.098 5.5 53723 53273 2 2
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 2.25 2.33 97.1 0.565 2.5 4.7
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 3d4i 2.25 47.95 50569 50569 2704 99.17 0.21068 0.20824 0.201 0.25672 0.2471 RANDOM 40.185
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] 0.53 0.8 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.078 r_dihedral_angle_4_deg 17.454 r_dihedral_angle_3_deg 17.249 r_dihedral_angle_1_deg 5.977 r_scangle_it 2.536 r_scbond_it 1.566 r_mcangle_it 1.318 r_angle_refined_deg 1.244 r_mcbond_it 0.704 r_metal_ion_refined 0.468
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.078 r_dihedral_angle_4_deg 17.454 r_dihedral_angle_3_deg 17.249 r_dihedral_angle_1_deg 5.977 r_scangle_it 2.536 r_scbond_it 1.566 r_mcangle_it 1.318 r_angle_refined_deg 1.244 r_mcbond_it 0.704 r_metal_ion_refined 0.468 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.157 r_chiral_restr 0.09 r_bond_refined_d 0.01 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_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 8414 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing