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Atomic resolution structure of apo-form of RafE from Streptococcus pneumoniae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 30% (w/v) PEG 4000, 0.1M Tris.HCl, 0.05M CaCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.19 43.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.219 α = 90 b = 129.315 β = 94.21 c = 119.42 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 MARMOSAIC 225 mm CCD 2005-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9393 ESRF BM14
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 1.04 19.82 97.6 0.062 9.8 4.12 543433 543433 8.8
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) 1.04 1.08 94.2 0.36 2.7 3.09 52441
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 MOLECULAR REPLACEMENT THROUGHOUT 1.04 19.82 543423 516098 27325 97.58 0.131 0.131 0.13 0.1392 0.157 0.165 Extended from low resolution model 11.116
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] -0.19 0.39 0.08 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.971 r_sphericity_free 15.103 r_dihedral_angle_3_deg 14.037 r_dihedral_angle_4_deg 9.09 r_dihedral_angle_1_deg 6.024 r_sphericity_bonded 5.939 r_scangle_it 5.732 r_angle_other_deg 4.247 r_scbond_it 4.239 r_mcbond_other 4.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.971 r_sphericity_free 15.103 r_dihedral_angle_3_deg 14.037 r_dihedral_angle_4_deg 9.09 r_dihedral_angle_1_deg 6.024 r_sphericity_bonded 5.939 r_scangle_it 5.732 r_angle_other_deg 4.247 r_scbond_it 4.239 r_mcbond_other 4.041 r_rigid_bond_restr 3.097 r_mcangle_it 3.057 r_angle_refined_deg 2.323 r_mcbond_it 2.263 r_symmetry_vdw_other 0.314 r_symmetry_hbond_refined 0.294 r_symmetry_vdw_refined 0.287 r_nbd_refined 0.267 r_nbd_other 0.249 r_xyhbond_nbd_refined 0.211 r_nbtor_refined 0.191 r_chiral_restr 0.14 r_nbtor_other 0.114 r_metal_ion_refined 0.077 r_bond_refined_d 0.029 r_gen_planes_other 0.015 r_gen_planes_refined 0.012 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10310 Nucleic Acid Atoms Solvent Atoms 2552 Heterogen Atoms 13
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ProDC data collection