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Staph. aureus DHFR F98Y complexed with AR-102
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FY8 PDB ENTRY 3FY8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 25% PEG3350, 200mM NaCl, 100mM bis-Tris, pH5.5
Crystal Properties Matthews coefficient Solvent content 2.72 54.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.432 α = 90 b = 79.432 β = 90 c = 108.597 γ = 120
Symmetry Space Group P 61 2 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2007-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.25 20 91.6 0.181 0.181 9334 8692 1.6 1.6
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 3FY8 2.25 20 8692 441 90.26 0.22268 0.21852 0.2293 0.3023 0.3207 RANDOM 31.225
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] -0.07 -0.04 -0.07 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.602 r_dihedral_angle_3_deg 22.814 r_dihedral_angle_4_deg 19.193 r_dihedral_angle_1_deg 10.933 r_angle_refined_deg 1.211 r_mcangle_it 1.113 r_angle_other_deg 0.909 r_mcbond_it 0.892 r_scangle_it 0.888 r_scbond_it 0.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.602 r_dihedral_angle_3_deg 22.814 r_dihedral_angle_4_deg 19.193 r_dihedral_angle_1_deg 10.933 r_angle_refined_deg 1.211 r_mcangle_it 1.113 r_angle_other_deg 0.909 r_mcbond_it 0.892 r_scangle_it 0.888 r_scbond_it 0.572 r_symmetry_hbond_refined 0.35 r_symmetry_vdw_other 0.34 r_nbd_other 0.279 r_xyhbond_nbd_refined 0.278 r_nbd_refined 0.273 r_symmetry_vdw_refined 0.262 r_nbtor_refined 0.2 r_mcbond_other 0.131 r_nbtor_other 0.096 r_chiral_restr 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_other_d r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1273 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 74
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALA data scaling