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Crystal Structure of the Group B Streptococcus Pullulanase SAP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FGZ PDB ENTRY 2FGZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 30% PEG3K, 0.2M CaCl2, 0.1M HEPES, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.949 α = 90 b = 102.834 β = 90 c = 172.438 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 110 CCD ADSC QUANTUM 315 2008-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 40 95.6 0.117 0.117 8.5 2.9 140381 49187 18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.2 98.1 0.258 0.258 3 2.8 7315
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 2FGZ 2.1 40 46648 2514 94.86 0.19576 0.19366 0.2002 0.23504 0.2431 RANDOM 13.368
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] 2.15 0.28 -2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.26 r_dihedral_angle_4_deg 15.195 r_dihedral_angle_3_deg 11.107 r_dihedral_angle_1_deg 8.96 r_scangle_it 3.039 r_scbond_it 2.184 r_mcangle_it 1.441 r_mcbond_it 1.029 r_angle_refined_deg 0.981 r_angle_other_deg 0.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.26 r_dihedral_angle_4_deg 15.195 r_dihedral_angle_3_deg 11.107 r_dihedral_angle_1_deg 8.96 r_scangle_it 3.039 r_scbond_it 2.184 r_mcangle_it 1.441 r_mcbond_it 1.029 r_angle_refined_deg 0.981 r_angle_other_deg 0.814 r_mcbond_other 0.222 r_nbd_refined 0.188 r_nbd_other 0.175 r_symmetry_vdw_other 0.172 r_nbtor_refined 0.167 r_symmetry_vdw_refined 0.142 r_symmetry_hbond_refined 0.124 r_xyhbond_nbd_refined 0.106 r_metal_ion_refined 0.094 r_nbtor_other 0.079 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6145 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 9
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling