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Crystal structure of a pheromone cOB1 precursor/lipoprotein, YaeC family (EF2496) from Enterococcus faecalis V583 at 2.10 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293 30.0% polyethylene glycol 400, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 46.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.225 α = 90 b = 75.691 β = 90 c = 143.815 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 x-ray 100 PIXEL DECTRIS PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2012-02-08 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97966,0.97901 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 2.1 28.763 90.6 0.04 12.37 28845 -3 38.876
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 2.1 2.17 64.9 0.746 1.4
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 2.1 28.763 28794 1458 95.25 0.1898 0.1875 0.1953 0.2322 0.2374 RANDOM 52.5789
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] -3.82 -0.87 4.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.808 r_dihedral_angle_4_deg 14.003 r_dihedral_angle_3_deg 12.346 r_dihedral_angle_1_deg 5.359 r_angle_refined_deg 1.858 r_angle_other_deg 1.465 r_nbd_other 0.215 r_nbd_refined 0.214 r_nbtor_refined 0.171 r_symmetry_vdw_other 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.808 r_dihedral_angle_4_deg 14.003 r_dihedral_angle_3_deg 12.346 r_dihedral_angle_1_deg 5.359 r_angle_refined_deg 1.858 r_angle_other_deg 1.465 r_nbd_other 0.215 r_nbd_refined 0.214 r_nbtor_refined 0.171 r_symmetry_vdw_other 0.14 r_symmetry_vdw_refined 0.122 r_nbtor_other 0.108 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3746 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 68
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling REFMAC refinement XDS data reduction SHELXD phasing