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Stationary Phase Survival Protein YuiC from B.subtilis complexed with NAG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AE0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 289 5mM NAG, 48% (v/v) polypropylene glycol P400, 0.1M HEPES pH 6, 3% (v/v) DMSO
Crystal Properties Matthews coefficient Solvent content 2.07 40.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.48 α = 90 b = 145.48 β = 90 c = 37.82 γ = 120
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 PSI PILATUS 6M 2013-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.21 36.37 98.8 0.043 10.3 3.2 89967 89967
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.21 1.23 97.2 0.569 2.4 3.2
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 2ae0 1.21 72.74 85213 4468 98.45 0.11235 0.1107 0.1146 0.14434 0.146 RANDOM 23.243
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] -0.01 -0.01 -0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.948 r_dihedral_angle_2_deg 32.603 r_dihedral_angle_4_deg 16.429 r_sphericity_bonded 16.337 r_dihedral_angle_3_deg 12.994 r_long_range_B_refined 7.537 r_long_range_B_other 7.371 r_dihedral_angle_1_deg 6.775 r_rigid_bond_restr 6.608 r_scangle_other 6.558
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.948 r_dihedral_angle_2_deg 32.603 r_dihedral_angle_4_deg 16.429 r_sphericity_bonded 16.337 r_dihedral_angle_3_deg 12.994 r_long_range_B_refined 7.537 r_long_range_B_other 7.371 r_dihedral_angle_1_deg 6.775 r_rigid_bond_restr 6.608 r_scangle_other 6.558 r_scbond_it 5.755 r_scbond_other 5.753 r_mcangle_it 5.571 r_mcangle_other 5.571 r_mcbond_other 4.438 r_mcbond_it 4.433 r_angle_refined_deg 2.156 r_angle_other_deg 1.183 r_chiral_restr 0.146 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_gen_planes_other 0.005 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2296 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling ACORN phasing