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Crystal structure of a duf1989 family protein (spo0365) from silicibacter pomeroyi dss-3 at 1.60 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 277 1.7M ammonium sulfate, 2.0% polyethylene glycol 400, 15.0% Glycerol, 0.1M HEPES pH 6.9, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.16 43.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.465 α = 90 b = 95.764 β = 109.04 c = 58.689 γ = 90
Symmetry Space Group P 1 21 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 325 mm CCD Flat mirror (vertical focusing) 2008-05-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97941,0.97904 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 28.41 98.3 0.072 0.072 7 2.6 69473 15.579
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 94 0.444 0.444 1.7 2.5 4868
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.6 28.41 69445 3499 98.15 0.142 0.141 0.1484 0.175 0.1787 RANDOM 12.623
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] 0.03 0.24 0.1 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.066 r_dihedral_angle_4_deg 15.417 r_dihedral_angle_3_deg 11.904 r_dihedral_angle_1_deg 6.127 r_scangle_it 4.587 r_scbond_it 3.317 r_mcangle_it 2.302 r_mcbond_it 1.616 r_angle_refined_deg 1.539 r_angle_other_deg 0.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.066 r_dihedral_angle_4_deg 15.417 r_dihedral_angle_3_deg 11.904 r_dihedral_angle_1_deg 6.127 r_scangle_it 4.587 r_scbond_it 3.317 r_mcangle_it 2.302 r_mcbond_it 1.616 r_angle_refined_deg 1.539 r_angle_other_deg 0.989 r_mcbond_other 0.57 r_symmetry_vdw_other 0.306 r_symmetry_vdw_refined 0.217 r_nbd_other 0.21 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.195 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.173 r_xyhbond_nbd_other 0.145 r_chiral_restr 0.095 r_nbtor_other 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4245 Nucleic Acid Atoms Solvent Atoms 739 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing