☰ Navigation Tabs
Crystal structure of sortase C-1 (SrtC-1) mutant H131D from S. pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W1J PDB ENTRY 2W1J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 293 100 MM TRIS-HCL PH 8.5, 200 MM MGCL2 HEXAHYDRATE, 30% W/V POLYETHYLENE GLYCOL 4000 AT 20C.
Crystal Properties Matthews coefficient Solvent content 2.2 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.348 α = 90 b = 70.523 β = 90 c = 87.278 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 CCD ADSC CCD 2008-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.3 50 95.3 0.05 17 4.8 99255 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 1.3 3.89 88.9 0.36 4.19 4.7
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 2W1J 1.3 19.81 98430 5137 99.49 0.15962 0.15776 0.1583 0.19533 0.195 RANDOM 14.989
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] -0.3 -0.12 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.274 r_dihedral_angle_4_deg 15.071 r_dihedral_angle_3_deg 12.156 r_dihedral_angle_1_deg 6.163 r_sphericity_free 4.536 r_scangle_it 3.504 r_sphericity_bonded 3.385 r_scbond_it 2.466 r_mcangle_it 1.754 r_angle_refined_deg 1.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.274 r_dihedral_angle_4_deg 15.071 r_dihedral_angle_3_deg 12.156 r_dihedral_angle_1_deg 6.163 r_sphericity_free 4.536 r_scangle_it 3.504 r_sphericity_bonded 3.385 r_scbond_it 2.466 r_mcangle_it 1.754 r_angle_refined_deg 1.406 r_rigid_bond_restr 1.402 r_mcbond_it 1.188 r_nbtor_refined 0.311 r_xyhbond_nbd_refined 0.219 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.185 r_symmetry_hbond_refined 0.162 r_chiral_restr 0.094 r_bond_refined_d 0.01 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3083 Nucleic Acid Atoms Solvent Atoms 693 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing