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Structure of RafE from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HFB PDB entry 2HFB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.8 295 2.8M (NaH2/K2H)PO4
0.1M Na acetate pH 3.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.61 52.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.754 α = 90 b = 77.7 β = 90 c = 79.226 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 2005-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9760 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 1.4 19.19 99 0.043 11.5 3.84 89237 89237
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 1.4 1.45 97 0.362 2.5 2.67 8648
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-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 PDB entry 2HFB 1.4 19.13 89229 89229 4460 99.02 0.163 0.163 0.161 0.1708 0.201 0.2081 RANDOM 23.196
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] 0.08 1.49 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.73 r_sphericity_free 15.174 r_dihedral_angle_3_deg 14.545 r_dihedral_angle_4_deg 10.535 r_dihedral_angle_1_deg 5.545 r_scangle_it 5.349 r_scbond_it 4.219 r_angle_other_deg 4.118 r_sphericity_bonded 4.035 r_mcangle_it 2.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.73 r_sphericity_free 15.174 r_dihedral_angle_3_deg 14.545 r_dihedral_angle_4_deg 10.535 r_dihedral_angle_1_deg 5.545 r_scangle_it 5.349 r_scbond_it 4.219 r_angle_other_deg 4.118 r_sphericity_bonded 4.035 r_mcangle_it 2.972 r_rigid_bond_restr 2.726 r_mcbond_other 2.423 r_mcbond_it 2.324 r_angle_refined_deg 2.023 r_symmetry_vdw_other 0.3 r_metal_ion_refined 0.291 r_nbd_refined 0.245 r_nbd_other 0.234 r_symmetry_vdw_refined 0.21 r_symmetry_hbond_refined 0.209 r_nbtor_refined 0.193 r_chiral_restr 0.152 r_xyhbond_nbd_refined 0.152 r_nbtor_other 0.111 r_bond_refined_d 0.024 r_gen_planes_other 0.022 r_gen_planes_refined 0.013 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3060 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 13
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction d*TREK data reduction