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Crystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex with adenosine and phosphate bound to the catalytic metal at 1.2 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N8N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 AphA 6mg/mL, 50 mM Na acetate, 25% PEG 6000, 10mM AMP, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.971 α = 90 b = 66.868 β = 116.96 c = 86.12 γ = 90
Symmetry Space Group C 1 2 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 4 channel - cut Si monochromator and cylindrical grazing incidence mirror 2002-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.96111 ESRF ID29
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 1.25 76.71 88.7 0.069 0.069 5.1 2.6 112327 112327 8.827
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.32 58.2 0.22 0.22 3 1.8 10703
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1N8N 1.25 76.71 104254 104254 8072 100 0.16693 0.16693 0.16527 0.1665 0.1885 0.1906 RANDOM 13.61
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] 0.11 0.26 0.07 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.941 r_dihedral_angle_4_deg 14.689 r_dihedral_angle_3_deg 11.231 r_dihedral_angle_1_deg 5.172 r_scangle_it 2.202 r_sphericity_free 1.703 r_sphericity_bonded 1.616 r_scbond_it 1.446 r_angle_refined_deg 1.391 r_mcangle_it 1.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.941 r_dihedral_angle_4_deg 14.689 r_dihedral_angle_3_deg 11.231 r_dihedral_angle_1_deg 5.172 r_scangle_it 2.202 r_sphericity_free 1.703 r_sphericity_bonded 1.616 r_scbond_it 1.446 r_angle_refined_deg 1.391 r_mcangle_it 1.043 r_rigid_bond_restr 0.813 r_mcbond_it 0.647 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.198 r_nbd_refined 0.183 r_symmetry_hbond_refined 0.08 r_chiral_restr 0.077 r_xyhbond_nbd_refined 0.076 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3314 Nucleic Acid Atoms Solvent Atoms 856 Heterogen Atoms 50
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling