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Structure of the Phosphatase Domain of the Cell Fate Determinant SpoIIE from Bacillus subtilis in a crystal form without domain swapping
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T9L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 2M Sodium formate, 0.1M Sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.57 52.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.285 α = 90 b = 122.506 β = 90 c = 81.617 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS3 S 6M 2012-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97950 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 2.44 61.34 99.7 0.057 0.999 20.1 6.3 10961
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.48 99.8 0.874 2.8 6.2
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 3T9L 2.45 48.99 10188 512 99.86 0.21386 0.21055 0.2107 0.27751 0.2698 RANDOM 66.958
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] -4.16 3.07 1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.932 r_dihedral_angle_4_deg 26.432 r_dihedral_angle_3_deg 20.01 r_long_range_B_other 10.978 r_long_range_B_refined 10.973 r_scangle_other 8.448 r_dihedral_angle_1_deg 7.515 r_mcangle_other 6.922 r_mcangle_it 6.919 r_scbond_it 5.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.932 r_dihedral_angle_4_deg 26.432 r_dihedral_angle_3_deg 20.01 r_long_range_B_other 10.978 r_long_range_B_refined 10.973 r_scangle_other 8.448 r_dihedral_angle_1_deg 7.515 r_mcangle_other 6.922 r_mcangle_it 6.919 r_scbond_it 5.317 r_scbond_other 5.314 r_mcbond_it 4.501 r_mcbond_other 4.433 r_angle_refined_deg 1.648 r_angle_other_deg 0.991 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1761 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing