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Crystal structure of a duf1831 family protein (lp2179) from lactobacillus plantarum at 1.20 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 10.5 277 0.2M NaCl, 20.0% PEG-8000, 0.1M CAPS, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K, pH 10.5 2 VAPOR DIFFUSION, SITTING DROP, NANODROP 9 277 20.0% PEG-6000, 0.1M Bicine, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K, pH 9.0
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.289 α = 90 b = 47.896 β = 90 c = 58.01 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 100 CCD ADSC QUANTUM 315 2006-08-31 2 2 x-ray 100 CCD MARMOSAIC 300 mm CCD Adjustable focusing mirrors in K-B geometry 2006-08-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9798 ALS 8.2.2 2 SYNCHROTRON APS BEAMLINE 23-ID-D 0.94926,0.97939,0.97925 APS 23-ID-D
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 2 1.198 28.928 90.4 0.069 0.069 6.1 6.2 29115
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) 2 1.2 1.23 50.7 0.204 0.204 3.7 1.4 1165
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 1.2 28.928 29080 1488 90.06 0.121 0.12 0.1249 0.147 0.1515 RANDOM 8.861
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] 0.85 -0.06 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.103 r_dihedral_angle_4_deg 15.509 r_dihedral_angle_3_deg 12.632 r_sphericity_free 8.569 r_dihedral_angle_1_deg 5.894 r_scangle_it 5.678 r_scbond_it 4.84 r_sphericity_bonded 4.255 r_mcangle_it 3.211 r_mcbond_it 2.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.103 r_dihedral_angle_4_deg 15.509 r_dihedral_angle_3_deg 12.632 r_sphericity_free 8.569 r_dihedral_angle_1_deg 5.894 r_scangle_it 5.678 r_scbond_it 4.84 r_sphericity_bonded 4.255 r_mcangle_it 3.211 r_mcbond_it 2.727 r_rigid_bond_restr 2.275 r_angle_refined_deg 1.646 r_mcbond_other 1.519 r_angle_other_deg 0.997 r_symmetry_vdw_other 0.293 r_nbd_refined 0.217 r_nbd_other 0.199 r_symmetry_vdw_refined 0.189 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.129 r_chiral_restr 0.097 r_nbtor_other 0.09 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 885 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 6
Software Software Software Name Purpose MolProbity model building SOLVE phasing REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling