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Crystal structure Analysis of the Streptococcus pneumoniae AdcAII protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 PEG 2000, NaCl, citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.76 α = 90 b = 63.26 β = 90 c = 151.66 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 QUANTUM 315 2007-06-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.971968, 0.979648, 0.979896 ESRF BM30A
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 2.4 44.9 95.6 0.044 0.071 12.91 3.7 40540 38743 2 13.3
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) 2.4 2.5 66.9 0.53 0.52 2.4 3.6 3981
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.4 44.9 21262 1064 100 0.229 0.225 0.2241 0.295 0.2932 RANDOM 56.198
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] 4.85 -3.72 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.004 r_dihedral_angle_3_deg 22.167 r_dihedral_angle_4_deg 22.113 r_dihedral_angle_1_deg 11.037 r_scangle_it 4.143 r_mcangle_it 2.841 r_scbond_it 2.481 r_angle_refined_deg 1.722 r_mcbond_it 1.602 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.004 r_dihedral_angle_3_deg 22.167 r_dihedral_angle_4_deg 22.113 r_dihedral_angle_1_deg 11.037 r_scangle_it 4.143 r_mcangle_it 2.841 r_scbond_it 2.481 r_angle_refined_deg 1.722 r_mcbond_it 1.602 r_nbtor_refined 0.315 r_nbd_refined 0.283 r_symmetry_vdw_refined 0.274 r_xyhbond_nbd_refined 0.215 r_metal_ion_refined 0.176 r_chiral_restr 0.172 r_symmetry_hbond_refined 0.165 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4132 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling SHARP phasing