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Crystal structure of dihydroneopterin aldolase from Bacillus anthracis complex with 9-METHYLGUANINE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NM2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 297 0.2 M Ammonium acetate,
0.1M Bis-Tris,
25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.52 51.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.795 α = 90 b = 138.209 β = 89.97 c = 63.933 γ = 90
Symmetry Space Group P 1 21 1
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 QUANTUM 315r 2015-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 45.21 84.7 0.111 0.124 0.055 7.5 4.6 62246
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 67.1 0.585 0.662 0.303 0.76 3.9 2443
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 2NM2 2 45.17 59338 3024 83.5 0.19494 0.19312 0.1906 0.23253 0.2318 RANDOM 47.535
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] -40.64 -5.05 89.11 -48.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.005 r_dihedral_angle_3_deg 16.105 r_dihedral_angle_4_deg 14.111 r_dihedral_angle_1_deg 7.379 r_long_range_B_refined 5.057 r_long_range_B_other 5.042 r_angle_refined_deg 1.468 r_mcangle_it 1.296 r_mcangle_other 1.296 r_scangle_other 0.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.005 r_dihedral_angle_3_deg 16.105 r_dihedral_angle_4_deg 14.111 r_dihedral_angle_1_deg 7.379 r_long_range_B_refined 5.057 r_long_range_B_other 5.042 r_angle_refined_deg 1.468 r_mcangle_it 1.296 r_mcangle_other 1.296 r_scangle_other 0.945 r_angle_other_deg 0.93 r_mcbond_it 0.728 r_mcbond_other 0.728 r_scbond_it 0.586 r_scbond_other 0.586 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7831 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-3000 data reduction MOLREP phasing BUCCANEER model building Coot model building