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Tandem GerMN domains of the sporulation protein GerM from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GZ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293.15 100 mM Hepes pH 7.2
2.6 M NH4SO4
Crystal Properties Matthews coefficient Solvent content 2.57 52.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.36 α = 90 b = 103.94 β = 90 c = 162.49 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 273 PIXEL DECTRIS PILATUS 6M 2017-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.07252 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 2.1 50 99.8 0.059 0.065 17.83 6 89726 45.52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.22 99.4 0.538 0.59 3.14 5.8
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 FREE R-VALUE 6GZ8 2.1 46.46 86153 3583 99.83 0.2049 0.2036 0.215 0.23621 0.2472 RANDOM 50.137
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] 2.03 -1.54 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.279 r_dihedral_angle_4_deg 17.572 r_dihedral_angle_3_deg 17.302 r_long_range_B_refined 12.388 r_long_range_B_other 12.387 r_scangle_other 10.672 r_mcangle_other 8.652 r_mcangle_it 8.65 r_scbond_it 8.238 r_scbond_other 8.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.279 r_dihedral_angle_4_deg 17.572 r_dihedral_angle_3_deg 17.302 r_long_range_B_refined 12.388 r_long_range_B_other 12.387 r_scangle_other 10.672 r_mcangle_other 8.652 r_mcangle_it 8.65 r_scbond_it 8.238 r_scbond_other 8.237 r_dihedral_angle_1_deg 6.957 r_mcbond_it 6.871 r_mcbond_other 6.842 r_angle_refined_deg 0.74 r_angle_other_deg 0.5 r_chiral_restr 0.051 r_gen_planes_refined 0.007 r_bond_refined_d 0.004 r_gen_planes_other 0.001 r_bond_other_d 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 8776 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing