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The structure of Streptococcus pneumoniae A153P ClpP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TYF PDB ENTRY 1TYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 PEG 400, Calcium acetate, cacodylate, pH 7.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.451 49.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.65 α = 90 b = 105.65 β = 90 c = 236.192 γ = 120
Symmetry Space Group P 32 2 1
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 2001-11-05 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 0.9675,0.9950 APS 32-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 29.5 0.056 16.6 5.6 47508 47508
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 71.1 0.239 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD + MR THROUGHOUT PDB ENTRY 1TYF 2.51 29.5 47508 42825 4680 88.99 0.19222 0.18598 0.194 0.24814 0.2512 RANDOM 30.917
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] 0.83 0.41 0.83 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.533 r_scangle_it 2.657 r_scbond_it 1.574 r_angle_refined_deg 1.302 r_mcangle_it 1.132 r_angle_other_deg 0.789 r_mcbond_it 0.591 r_symmetry_hbond_refined 0.288 r_nbd_other 0.222 r_symmetry_vdw_other 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.533 r_scangle_it 2.657 r_scbond_it 1.574 r_angle_refined_deg 1.302 r_mcangle_it 1.132 r_angle_other_deg 0.789 r_mcbond_it 0.591 r_symmetry_hbond_refined 0.288 r_nbd_other 0.222 r_symmetry_vdw_other 0.2 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.168 r_symmetry_vdw_refined 0.143 r_metal_ion_refined 0.121 r_nbtor_other 0.086 r_chiral_restr 0.072 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9449 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNX phasing CNX refinement