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Crystal structure of a protein from the duf1801 family (ydhg, bsu05750) from bacillus subtilis at 1.75 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 277 32.0% polyethylene glycol 8000, 0.25M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.37 48.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.782 α = 90 b = 46.903 β = 110.05 c = 64.568 γ = 90
Symmetry Space Group P 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD Adjustable focusing mirrors in K-B geometry 2006-10-20 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97921, 0.97942 APS 23-ID-D
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 1.75 37.113 85.1 0.078 10.9 3.2 23448
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 1.75 1.81 40.2 0.322 1.9 1105
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.75 37.113 23443 1168 84.13 0.175 0.173 0.217 0.2637 RANDOM 30.168
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] 0.98 1.91 -0.16 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.202 r_dihedral_angle_4_deg 25.692 r_dihedral_angle_3_deg 10.888 r_dihedral_angle_1_deg 5.494 r_scangle_it 4.683 r_scbond_it 3.8 r_mcangle_it 2.212 r_mcbond_it 1.653 r_angle_refined_deg 1.274 r_angle_other_deg 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.202 r_dihedral_angle_4_deg 25.692 r_dihedral_angle_3_deg 10.888 r_dihedral_angle_1_deg 5.494 r_scangle_it 4.683 r_scbond_it 3.8 r_mcangle_it 2.212 r_mcbond_it 1.653 r_angle_refined_deg 1.274 r_angle_other_deg 0.76 r_mcbond_other 0.402 r_symmetry_vdw_other 0.266 r_nbd_refined 0.204 r_nbtor_refined 0.185 r_nbd_other 0.167 r_xyhbond_nbd_refined 0.162 r_symmetry_vdw_refined 0.157 r_symmetry_hbond_refined 0.109 r_nbtor_other 0.082 r_chiral_restr 0.079 r_xyhbond_nbd_other 0.029 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2000 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 59
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction autoSHARP phasing SHELXD phasing