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Crystal structure of a protein of unknown function (NP_472245.1) from Listeria innocua at 1.65 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 277 1.6M (NH4)2SO4, 0.1M Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.57 52.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.03 α = 90 b = 100.03 β = 90 c = 62.74 γ = 120
Symmetry Space Group P 63 2 2
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 2006-08-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.94926,0.97925 APS 23-ID-D
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 1.65 29.501 99.6 0.094 9.89 22770 30.934
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 1.65 1.71 97.8 0.01117 1.35 3602
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 1.65 29.501 22751 1165 99.74 0.2 0.198 0.2004 0.235 0.2337 RANDOM 23.603
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] -1.69 -0.85 -1.69 2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.967 r_dihedral_angle_4_deg 16.049 r_dihedral_angle_3_deg 13.334 r_scangle_it 6.784 r_dihedral_angle_1_deg 5.686 r_scbond_it 5.078 r_mcangle_it 3.08 r_mcbond_it 2.383 r_angle_refined_deg 1.526 r_angle_other_deg 0.947
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.967 r_dihedral_angle_4_deg 16.049 r_dihedral_angle_3_deg 13.334 r_scangle_it 6.784 r_dihedral_angle_1_deg 5.686 r_scbond_it 5.078 r_mcangle_it 3.08 r_mcbond_it 2.383 r_angle_refined_deg 1.526 r_angle_other_deg 0.947 r_mcbond_other 0.611 r_symmetry_hbond_refined 0.29 r_symmetry_vdw_other 0.226 r_symmetry_vdw_refined 0.213 r_nbd_refined 0.206 r_nbd_other 0.191 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.09 r_nbtor_other 0.089 r_bond_refined_d 0.018 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 1220 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 6
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing SOLVE phasing