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Structure of the S. agalactiae serine/threonine phosphatase at 2.65 resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Manually built model from SAD phasing = S.a. STP with 70% of residues built
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.2 M Mg acetate, 18% PEG 8000, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.54 51.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.4 α = 90 b = 92.1 β = 90 c = 86.9 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2005-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 ESRF ID14-1
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 2.65 20 99.5 0.115 0.115 11.7 5.2 32931 32767 2 3 50
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 2.65 2.7 99 0.44 0.44 3.7 4.2 7442
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 Manually built model from SAD phasing = S.a. STP with 70% of residues built 2.65 19.65 2 2 32000 31351 1651 100 0.20046 0.2 0.19667 0.196 0.27121 0.2673 RANDOM 42.058
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] 0.17 0.09 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.097 r_dihedral_angle_4_deg 18.728 r_dihedral_angle_3_deg 16.979 r_dihedral_angle_1_deg 6.147 r_scangle_it 2.918 r_mcangle_it 2.901 r_scbond_it 1.915 r_mcbond_it 1.827 r_angle_refined_deg 1.313 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.097 r_dihedral_angle_4_deg 18.728 r_dihedral_angle_3_deg 16.979 r_dihedral_angle_1_deg 6.147 r_scangle_it 2.918 r_mcangle_it 2.901 r_scbond_it 1.915 r_mcbond_it 1.827 r_angle_refined_deg 1.313 r_nbtor_refined 0.313 r_symmetry_hbond_refined 0.276 r_xyhbond_nbd_refined 0.178 r_nbd_refined 0.146 r_symmetry_vdw_refined 0.114 r_metal_ion_refined 0.1 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7468 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection XDS data reduction XSCALE data scaling MOLREP phasing