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Serine protease SplB from Staphylococcus aureus at 1.8A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AS9 PDB ENTRY 2AS9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 SITTING DROP VAPOR DIFFUSION; 20C; GROWN BY MIXING EQUAL VOLUMES OF SPLB (35 MG/ML IN 5MM TRIS-HCL, PH 8.0 CONTAINING 50MM NACL) AND 0.1M TRIS-HCL, PH 8.5-9.0 CONTAINING 30% PEG 3350 (OPTIMIZED HAMPTON RESEARCH INDEX SOLUTION NUMBER 45)
Crystal Properties Matthews coefficient Solvent content 2.69 53.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.475 α = 90 b = 117.475 β = 90 c = 73.293 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 MARRESEARCH 2006-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 MPG/DESY, HAMBURG BW6
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 1.8 20 99 0.06 29.4 14.4 48001 2
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 1.8 1.9 99 0.35 4.2 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2AS9 1.8 20 45454 2403 99.8 0.213 0.211 0.2109 0.253 0.2506 RANDOM 26.62
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] 0.91 0.91 -1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33 r_dihedral_angle_4_deg 22.105 r_dihedral_angle_3_deg 13.203 r_dihedral_angle_1_deg 6.629 r_scangle_it 3.736 r_scbond_it 2.614 r_mcangle_it 1.804 r_angle_refined_deg 1.516 r_mcbond_it 1.093 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33 r_dihedral_angle_4_deg 22.105 r_dihedral_angle_3_deg 13.203 r_dihedral_angle_1_deg 6.629 r_scangle_it 3.736 r_scbond_it 2.614 r_mcangle_it 1.804 r_angle_refined_deg 1.516 r_mcbond_it 1.093 r_nbtor_refined 0.313 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.111 r_symmetry_hbond_refined 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3032 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing