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Crystal structure of a signal peptidase I (EF3073) from Enterococcus faecalis V583 at 2.27 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 20.00% polyethylene glycol 3350, 0.200M ammonium fluoride, No Buffer pH 6.2, Additive: 0.001 M leupeptin, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.73 28.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.488 α = 90 b = 37.488 β = 90 c = 169.046 γ = 90
Symmetry Space Group P 41 21 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 325 mm CCD Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing) 2011-01-26 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97944,0.97894 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 2.27 28.174 99.4 0.077 11.93 6200 -3 47.346
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 2.27 2.35 99.1 0.777 1.7
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 2.27 28.174 6146 486 99.53 0.2162 0.2124 0.2184 0.258 0.2556 RANDOM 61.7506
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] 1.91 1.91 -3.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.677 r_dihedral_angle_3_deg 15.055 r_dihedral_angle_4_deg 11.706 r_dihedral_angle_1_deg 6.606 r_mcangle_it 1.935 r_angle_refined_deg 1.229 r_mcbond_other 1.173 r_mcbond_it 1.172 r_angle_other_deg 0.786 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.677 r_dihedral_angle_3_deg 15.055 r_dihedral_angle_4_deg 11.706 r_dihedral_angle_1_deg 6.606 r_mcangle_it 1.935 r_angle_refined_deg 1.229 r_mcbond_other 1.173 r_mcbond_it 1.172 r_angle_other_deg 0.786 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 904 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 8
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing REFMAC refinement XDS data reduction XSCALE data scaling SHELXD phasing