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Cell surface protein YwfG protein (apo form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M01
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M sodium acetate (pH 5.0-5.6),
1.3 M Li2SO4,
2% (w/v) polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 4.37 71.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.219 α = 90 b = 272.93 β = 90 c = 320.332 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS3 S 6M 2018-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.5 48.6 100 0.092 0.096 0.026 0.999 21.3 13 66894
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 100 0.809 0.841 0.229 0.871 3.4 13.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4m01 2.5 45.53 66893 3224 99.969 0.247 0.2455 0.252 0.2796 0.2807 65.081
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] -5.041 4.543 0.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.665 r_dihedral_angle_3_deg 21.114 r_dihedral_angle_4_deg 17.235 r_lrange_it 13.365 r_lrange_other 13.359 r_scangle_it 10.846 r_scangle_other 10.719 r_mcangle_it 10.373 r_mcangle_other 10.373 r_scbond_it 7.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.665 r_dihedral_angle_3_deg 21.114 r_dihedral_angle_4_deg 17.235 r_lrange_it 13.365 r_lrange_other 13.359 r_scangle_it 10.846 r_scangle_other 10.719 r_mcangle_it 10.373 r_mcangle_other 10.373 r_scbond_it 7.47 r_scbond_other 7.352 r_mcbond_other 7.323 r_mcbond_it 7.322 r_dihedral_angle_1_deg 7.095 r_angle_refined_deg 1.754 r_angle_other_deg 1.345 r_metal_ion_refined 0.274 r_nbd_other 0.231 r_nbd_refined 0.202 r_symmetry_nbd_other 0.202 r_symmetry_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.171 r_symmetry_nbd_refined 0.162 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.065 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6527 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing