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Crystal Structure of RafE from Streptococcus pneumoniae complexed with raffinose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HQ0 2 models: 2HQ0 residues 1-114 and 278-327 and 2HQ0 residues 115-277 and 328-387
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 25.5% PEG4000
0.085M Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.47 50.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.214 α = 90 b = 119.435 β = 90 c = 146.326 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 MARMOSAIC 225 mm CCD mirrors 2006-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.5418
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 2.8 49.21 91.5 0.171 7 6.59 20180 20180
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 2.8 2.9 98.1 0.461 2.7 6.3 2121
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 (All) 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 2 models:
2HQ0 residues 1-114 and 278-327
and
2HQ0 residues 115-277 and 328-387 2.8 46.27 20129 20129 971 91.45 0.215 0.211 0.2156 0.296 0.2952 Conserved from 2HQ0 47.857
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] 3.46 3.84 -7.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.205 r_dihedral_angle_4_deg 19.697 r_dihedral_angle_3_deg 18.811 r_dihedral_angle_1_deg 7.166 r_mcbond_other 6.141 r_scangle_it 4.69 r_angle_other_deg 4.606 r_mcangle_it 3.175 r_scbond_it 2.921 r_mcbond_it 1.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.205 r_dihedral_angle_4_deg 19.697 r_dihedral_angle_3_deg 18.811 r_dihedral_angle_1_deg 7.166 r_mcbond_other 6.141 r_scangle_it 4.69 r_angle_other_deg 4.606 r_mcangle_it 3.175 r_scbond_it 2.921 r_mcbond_it 1.794 r_angle_refined_deg 1.756 r_symmetry_vdw_other 0.306 r_nbd_refined 0.245 r_symmetry_vdw_refined 0.244 r_nbd_other 0.24 r_nbtor_refined 0.2 r_xyhbond_nbd_refined 0.166 r_nbtor_other 0.122 r_chiral_restr 0.094 r_symmetry_hbond_refined 0.084 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6086 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 71
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection d*TREK data reduction