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Crystal structure of SusD homolog (NP_809186.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.35 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 277 0.2000M NaNO3, 20.0000% PEG-3350, No Buffer pH 6.8, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.12 41.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.65 α = 90 b = 74.37 β = 111.64 c = 67.375 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) 2009-04-16 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97848,0.97787 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 1.35 29.656 86.8 0.071 0.071 12.5 4 87986 12.865
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) 1.35 1.39 91.1 0.259 0.259 2.6 2 6668
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 1.35 29.656 87959 4361 86.51 0.147 0.146 0.1542 0.167 0.177 RANDOM 17.65
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] -0.16 -0.19 -0.42 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.396 r_dihedral_angle_4_deg 15.62 r_dihedral_angle_3_deg 11.639 r_dihedral_angle_1_deg 10.091 r_scangle_it 4.978 r_scbond_it 3.654 r_mcangle_it 2.239 r_mcbond_it 1.522 r_angle_refined_deg 1.417 r_angle_other_deg 0.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.396 r_dihedral_angle_4_deg 15.62 r_dihedral_angle_3_deg 11.639 r_dihedral_angle_1_deg 10.091 r_scangle_it 4.978 r_scbond_it 3.654 r_mcangle_it 2.239 r_mcbond_it 1.522 r_angle_refined_deg 1.417 r_angle_other_deg 0.859 r_mcbond_other 0.374 r_nbd_refined 0.268 r_symmetry_vdw_other 0.247 r_symmetry_hbond_refined 0.223 r_nbd_other 0.216 r_nbtor_refined 0.196 r_xyhbond_nbd_refined 0.189 r_nbtor_other 0.092 r_chiral_restr 0.087 r_symmetry_vdw_refined 0.085 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3887 Nucleic Acid Atoms Solvent Atoms 610 Heterogen Atoms 21
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