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Crystal structure of protein SP0239 from Streptococcus pneumoniae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 0.2 M NaCl, 0.1M Bis-Tris, 25 % PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.3 62.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.906 α = 90 b = 139.963 β = 90 c = 148.896 γ = 90
Symmetry Space Group C 2 2 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 QUANTUM 315 2005-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97915 APS 19-ID
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 2.7 50 95.5 0.104 23.14 6.1 33231 33065 -3
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 2.7 2.8 85 0.694 1.82 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.7 50 31354 31354 1672 95.41 0.19754 0.19376 0.1909 0.27127 0.2664 RANDOM 43.181
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] -1.08 -0.49 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.253 r_dihedral_angle_4_deg 24.691 r_dihedral_angle_3_deg 23.17 r_dihedral_angle_1_deg 9.338 r_scangle_it 7.069 r_scbond_it 4.611 r_angle_refined_deg 2.954 r_mcangle_it 2.601 r_mcbond_it 1.933 r_nbtor_refined 0.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.253 r_dihedral_angle_4_deg 24.691 r_dihedral_angle_3_deg 23.17 r_dihedral_angle_1_deg 9.338 r_scangle_it 7.069 r_scbond_it 4.611 r_angle_refined_deg 2.954 r_mcangle_it 2.601 r_mcbond_it 1.933 r_nbtor_refined 0.346 r_symmetry_vdw_refined 0.302 r_nbd_refined 0.301 r_symmetry_hbond_refined 0.198 r_chiral_restr 0.194 r_xyhbond_nbd_refined 0.174 r_bond_refined_d 0.035 r_gen_planes_refined 0.01 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5957 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement