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Crystal Structure of Conserved Protein of Unknown Function from Streptococcus pneumoniae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10 291 1.2M NaH2PO4
/0.8M K2HPO4
Caps 10.5
0.2M Li2So2
, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.95 36.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.665 α = 90 b = 62.359 β = 100.92 c = 63.415 γ = 90
Symmetry Space Group C 1 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 ADSC QUANTUM 315 mirrors 2006-08-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794,0.9795 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 1.7 40 91.5 0.057 21.3 4.2 22271 20526 31
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 1.7 1.73 0.25 3.6 2.3
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 (All) 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 MAD THROUGHOUT 1.7 40 20460 19397 1048 92.01 0.171 0.171 0.16758 0.1758 0.22637 0.2326 RANDOM 17.376
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] -0.87 0.91 -1.42 2.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.932 r_dihedral_angle_3_deg 13.772 r_dihedral_angle_4_deg 12.498 r_dihedral_angle_1_deg 6.515 r_scangle_it 2.897 r_scbond_it 1.852 r_angle_refined_deg 1.384 r_angle_other_deg 1.249 r_mcangle_it 1.196 r_mcbond_it 0.663
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.932 r_dihedral_angle_3_deg 13.772 r_dihedral_angle_4_deg 12.498 r_dihedral_angle_1_deg 6.515 r_scangle_it 2.897 r_scbond_it 1.852 r_angle_refined_deg 1.384 r_angle_other_deg 1.249 r_mcangle_it 1.196 r_mcbond_it 0.663 r_symmetry_vdw_other 0.237 r_chiral_restr 0.22 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.212 r_nbd_other 0.194 r_nbtor_refined 0.178 r_symmetry_hbond_refined 0.167 r_mcbond_other 0.161 r_xyhbond_nbd_refined 0.153 r_symmetry_metal_ion_refined 0.102 r_nbtor_other 0.085 r_metal_ion_refined 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1799 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building