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Crystal structure of a duf574 family protein (sav_2177) from streptomyces avermitilis ma-4680 at 1.80 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GIW PDB entry 3GIW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 NANODROP, 0.2M Sodium chloride, 2.0M Ammonium sulfate, 0.1M Sodium cacodylate pH 6.5, Additive: 0.001 M S-adenosyl-L-homocysteine, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.46 50.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.637 α = 90 b = 49.439 β = 123.8 c = 77.811 γ = 90
Symmetry Space Group C 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 325 mm CCD Flat mirror (vertical focusing) 2009-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837 SSRL BL11-1
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 1.8 27.482 95.3 0.099 26949 -3 15.486
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 1.8 1.86 92.4 0.478 1.6
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 PDB entry 3GIW 1.8 27.482 26949 1345 96.56 0.202 0.2 0.2022 0.25 0.2451 RANDOM 17.22
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] 3.12 0.59 -1.93 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.969 r_dihedral_angle_4_deg 12.681 r_dihedral_angle_3_deg 11.334 r_dihedral_angle_1_deg 3.619 r_scangle_it 1.945 r_mcangle_it 1.783 r_angle_refined_deg 1.63 r_scbond_it 1.26 r_mcbond_it 1.16 r_angle_other_deg 0.953
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.969 r_dihedral_angle_4_deg 12.681 r_dihedral_angle_3_deg 11.334 r_dihedral_angle_1_deg 3.619 r_scangle_it 1.945 r_mcangle_it 1.783 r_angle_refined_deg 1.63 r_scbond_it 1.26 r_mcbond_it 1.16 r_angle_other_deg 0.953 r_mcbond_other 0.31 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2023 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction MOLREP phasing