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Synthesis of CDP-activated ribitol for teichoic acid precursors in Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VPA PDB ENTRY 1VPA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.75 100 MM HEPES PH 6.75 35 % V/W PEG 300 200 MM CACL2
Crystal Properties Matthews coefficient Solvent content 2.42 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.94 α = 90 b = 92.38 β = 90 c = 143.58 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 140 IMAGE PLATE RIGAKU IMAGE PLATE MIRRORS 2008-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU R-AXIS
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 2.75 60.86 99.5 0.09 14.7 3.6 14243 2
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 2.75 2.9 100 0.52 2.2 3.6
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 PDB ENTRY 1VPA 2.75 56.08 12215 624 89.5 0.215 0.212 0.2086 0.271 0.2697 RANDOM 55.38
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] 1.27 -1.99 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.435 r_dihedral_angle_3_deg 17.262 r_dihedral_angle_4_deg 15.458 r_dihedral_angle_1_deg 5.543 r_angle_refined_deg 1.193 r_scangle_it 0.947 r_scbond_it 0.59 r_mcangle_it 0.459 r_nbtor_refined 0.303 r_mcbond_it 0.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.435 r_dihedral_angle_3_deg 17.262 r_dihedral_angle_4_deg 15.458 r_dihedral_angle_1_deg 5.543 r_angle_refined_deg 1.193 r_scangle_it 0.947 r_scbond_it 0.59 r_mcangle_it 0.459 r_nbtor_refined 0.303 r_mcbond_it 0.258 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.163 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.124 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3556 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing