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Escherichia coli Signal Peptidase I Delta 2-76 P84A in complex with lipopeptide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S04 PDN ENTRY 3S04
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 294.15 25%v/v PEG 4000, 0.05M NH4OAC, 0.1M NaOAc pH 4.6, 0.033M L-proline
Crystal Properties Matthews coefficient Solvent content 3.03 59.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.8 α = 90 b = 71.8 β = 90 c = 263.31 γ = 90
Symmetry Space Group P 43 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 RAYONIX MX-300 2012-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.1047 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.32 52.63 99.7 0.097 0.105 0.039 13 7.2 30863
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.45 99.8 0.392 0.422 0.154 5.8 7.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.32 35.596 30716 1119 99.266 0.21 0.2086 0.2135 0.2338 0.2343 42.583
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] 0.545 0.545 -1.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.446 r_dihedral_angle_3_deg 12.49 r_dihedral_angle_2_deg 10.448 r_lrange_other 7.911 r_lrange_it 7.908 r_dihedral_angle_1_deg 7.245 r_scangle_it 5.939 r_scangle_other 5.938 r_mcangle_it 5.511 r_mcangle_other 5.509
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.446 r_dihedral_angle_3_deg 12.49 r_dihedral_angle_2_deg 10.448 r_lrange_other 7.911 r_lrange_it 7.908 r_dihedral_angle_1_deg 7.245 r_scangle_it 5.939 r_scangle_other 5.938 r_mcangle_it 5.511 r_mcangle_other 5.509 r_scbond_it 3.786 r_scbond_other 3.785 r_mcbond_it 3.606 r_mcbond_other 3.603 r_angle_refined_deg 1.4 r_angle_other_deg 0.475 r_symmetry_nbd_other 0.197 r_nbd_refined 0.185 r_nbtor_refined 0.179 r_nbd_other 0.139 r_symmetry_nbd_refined 0.133 r_xyhbond_nbd_refined 0.132 r_symmetry_xyhbond_nbd_refined 0.114 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.064 r_symmetry_xyhbond_nbd_other 0.063 r_bond_refined_d 0.006 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 3478 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing