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Crystal structure of AphA class B acid phosphatase/phosphotransferase complexed with adenosine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N8N PDB entry 1N8N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 Crystallization components* AphA 6mg/mL, 50mM Na acetate, 25% PEG 6000, 10mM adenosine, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.74 α = 90 b = 66.704 β = 117.13 c = 88.556 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 4 2002-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.96111 ESRF ID14-1
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 1.4 75.419 0.099 0.099 3.7 3.4 153897 153897
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 1.4 1.48 59.3 0.452 0.452 1.6 2.3
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 (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 1N8N 1.4 74.54 142874 142874 11010 100 0.16906 0.16669 0.1736 0.19908 0.2036 RANDOM 11.611
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] 0.29 0.08 -0.33 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.791 r_scangle_it 3.574 r_sphericity_free 3.3 r_sphericity_bonded 2.386 r_scbond_it 2.368 r_mcangle_it 1.68 r_angle_refined_deg 1.558 r_rigid_bond_restr 1.285 r_mcbond_it 1.14 r_angle_other_deg 0.853
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.791 r_scangle_it 3.574 r_sphericity_free 3.3 r_sphericity_bonded 2.386 r_scbond_it 2.368 r_mcangle_it 1.68 r_angle_refined_deg 1.558 r_rigid_bond_restr 1.285 r_mcbond_it 1.14 r_angle_other_deg 0.853 r_symmetry_vdw_other 0.299 r_nbd_other 0.259 r_symmetry_vdw_refined 0.259 r_nbd_refined 0.22 r_symmetry_hbond_refined 0.216 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.087 r_nbtor_other 0.083 r_metal_ion_refined 0.018 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6590 Nucleic Acid Atoms Solvent Atoms 1233 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing