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Crystal structure of the choline binding domain of Spr1274 in Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V05
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 1.75M (NH4)2SO4, 0.1M MES, pH 6.5, 10% dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.7 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.61 α = 90 b = 140.61 β = 90 c = 46.05 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2008-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 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 2.3 70.36 0.072 14.26 3.79 15041 38.6
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 2.3 2.42 0.4 3.38 3.79 2205
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 2V05 2.38 20 11301 1627 94.81 0.22852 0.22306 0.2362 0.26509 0.273 RANDOM 34.538
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] -6.52 -3.26 -6.52 9.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.589 r_dihedral_angle_4_deg 34.408 r_dihedral_angle_3_deg 17.2 r_dihedral_angle_1_deg 5.968 r_scangle_it 1.966 r_scbond_it 1.367 r_angle_refined_deg 1.245 r_mcangle_it 1.065 r_mcbond_it 0.59 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.589 r_dihedral_angle_4_deg 34.408 r_dihedral_angle_3_deg 17.2 r_dihedral_angle_1_deg 5.968 r_scangle_it 1.966 r_scbond_it 1.367 r_angle_refined_deg 1.245 r_mcangle_it 1.065 r_mcbond_it 0.59 r_nbtor_refined 0.304 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_refined 0.185 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1807 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 52
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALEPACK data scaling