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The bifunctional dihydroneopterin aldolase 6-hydroxymethyl-7,8- dihydropterin synthase from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NBU PDB ENTRY 1NBU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 pH 7.00
Crystal Properties Matthews coefficient Solvent content 5.6 78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.44 α = 90 b = 149.44 β = 90 c = 238.74 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
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 2.87 42 99.9 0.11 9.4 6 62341 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 2.87 2.97 99.6 0.42 4.3 5.76
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NBU 2.9 127 57383 3059 99.8 0.216 0.215 0.241 RANDOM 46.97
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] 1.34 1.34 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.766 r_dihedral_angle_3_deg 20.571 r_dihedral_angle_4_deg 17.811 r_dihedral_angle_1_deg 7.29 r_scangle_it 3.287 r_angle_refined_deg 3.164 r_mcangle_it 2.576 r_scbond_it 2.258 r_mcbond_it 1.738 r_nbtor_refined 0.363
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.766 r_dihedral_angle_3_deg 20.571 r_dihedral_angle_4_deg 17.811 r_dihedral_angle_1_deg 7.29 r_scangle_it 3.287 r_angle_refined_deg 3.164 r_mcangle_it 2.576 r_scbond_it 2.258 r_mcbond_it 1.738 r_nbtor_refined 0.363 r_nbd_refined 0.291 r_symmetry_vdw_refined 0.266 r_chiral_restr 0.179 r_xyhbond_nbd_refined 0.164 r_symmetry_hbond_refined 0.153 r_bond_refined_d 0.04 r_gen_planes_refined 0.011 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 7968 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose CrystalClear data reduction CrystalClear data scaling MOLREP phasing CNS phasing REFMAC refinement