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Crystal structure of the 2H-phosphatase domain of Sts-2 in complex with phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D4I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20% PEG8000 (w/v), 0.2 M lithium sulfate, 5 to 20 mM strontium chloride, 0.1 M Tris-HCl. Soaked in 0.2 M Na/K phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.081 α = 90 b = 117.025 β = 90 c = 121.666 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 2006-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.00 NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.77 43.7 98.6 0.101 21 5.7 28541 28141 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.77 2.9 100 0.617 2.68 6
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 FOURIER SYNTHESIS THROUGHOUT 3D4I 2.77 43.69 26559 1429 96.92 0.24704 0.24581 0.2346 0.26998 0.2604 RANDOM 61.583
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 2.62 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.218 r_dihedral_angle_4_deg 16.045 r_dihedral_angle_3_deg 14.575 r_dihedral_angle_1_deg 5.177 r_scangle_it 2.72 r_mcangle_it 2.042 r_scbond_it 1.717 r_angle_refined_deg 1.379 r_mcbond_it 1.166 r_symmetry_vdw_refined 0.362
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.218 r_dihedral_angle_4_deg 16.045 r_dihedral_angle_3_deg 14.575 r_dihedral_angle_1_deg 5.177 r_scangle_it 2.72 r_mcangle_it 2.042 r_scbond_it 1.717 r_angle_refined_deg 1.379 r_mcbond_it 1.166 r_symmetry_vdw_refined 0.362 r_nbtor_refined 0.311 r_nbd_refined 0.23 r_symmetry_hbond_refined 0.204 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 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 8401 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing