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Crystal structure of a lipocalin-like protein (BT_0869) from Bacteroides thetaiotaomicron VPI-5482 at 1.95 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277 1.6000M (NH4)2SO4, 0.1M Citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 50.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.51 α = 90 b = 125.51 β = 90 c = 181.45 γ = 120
Symmetry Space Group P 31 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 2008-10-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.94645,0.97965 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.95 29.735 99.8 0.128 0.141 8.71 5.6 120441 -3 23.792
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.01 100 0.891 0.984 2.1
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 1.95 29.735 120381 6044 99.83 0.168 0.166 0.1754 0.206 0.211 RANDOM 38.121
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] 0.23 0.12 0.23 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.913 r_dihedral_angle_3_deg 11.122 r_dihedral_angle_4_deg 10.936 r_scangle_it 6.264 r_scbond_it 4.641 r_dihedral_angle_1_deg 3.499 r_mcangle_it 2.512 r_mcbond_it 1.834 r_angle_refined_deg 1.641 r_angle_other_deg 0.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.913 r_dihedral_angle_3_deg 11.122 r_dihedral_angle_4_deg 10.936 r_scangle_it 6.264 r_scbond_it 4.641 r_dihedral_angle_1_deg 3.499 r_mcangle_it 2.512 r_mcbond_it 1.834 r_angle_refined_deg 1.641 r_angle_other_deg 0.899 r_mcbond_other 0.554 r_symmetry_vdw_refined 0.221 r_symmetry_vdw_other 0.209 r_symmetry_hbond_refined 0.196 r_nbd_refined 0.186 r_nbd_other 0.181 r_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.17 r_xyhbond_nbd_other 0.114 r_symmetry_hbond_other 0.105 r_chiral_restr 0.088 r_nbtor_other 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11096 Nucleic Acid Atoms Solvent Atoms 1458 Heterogen Atoms 335
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing