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Staphylococcus aureus 7,8-Dihydro-6-hydroxymethylpterin- pyrophosphokinase in complex with AMPCPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AD6 PDB ENTRY 4AD6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 281 PROTEIN 6.9 MG/ML 1 MM AMPCPP, 2 MM MAGNESIUM CHLORIDE, MAGNESIUM ACETATE 0.119 M, PEG8000 12.6% W/V, TRIS CHLORIDE 0.12 M, SITTING DROP, 281 K
Crystal Properties Matthews coefficient Solvent content 2.39 48.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.002 α = 90 b = 94.263 β = 112.44 c = 62.989 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 CCD 2013-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 Australian Synchrotron MX2
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 2.7 45.53 100 0.14 9.4 7.5 18506
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 2.7 2.83 100 0.9 2.1 7.3
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 4AD6 2.7 45.53 17651 838 99.96 0.19433 0.19217 0.1957 0.24223 0.2451 RANDOM 54.203
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] 0.16 2.65 0.06 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.791 r_dihedral_angle_4_deg 16.655 r_dihedral_angle_3_deg 14.635 r_dihedral_angle_1_deg 6.304 r_angle_other_deg 3.437 r_angle_refined_deg 1.493 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.791 r_dihedral_angle_4_deg 16.655 r_dihedral_angle_3_deg 14.635 r_dihedral_angle_1_deg 6.304 r_angle_other_deg 3.437 r_angle_refined_deg 1.493 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 4999 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing