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Crystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex with deoxycytosine and phosphate bound to the catalytic metal
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, 50mM Na acetate, 25% PEG 6000, 10mM dCMP, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.882 α = 90 b = 66.393 β = 119.66 c = 90.018 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 MARRESEARCH Double crystal focusing monochromator 2003-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 1.05800 EMBL/DESY, HAMBURG BW7A
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 1.75 30.58 98.7 0.075 0.075 8.5 2.7 46824 46824 13.387
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 1.75 1.84 98 0.328 0.328 2.2 2.7 6759
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 1.75 30.57 42902 42902 3918 100 0.15647 0.15647 0.15312 0.1605 0.19361 0.198 RANDOM 14.504
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] 0.43 0.07 -0.69 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.496 r_scangle_it 4.162 r_scbond_it 2.554 r_angle_refined_deg 1.497 r_mcangle_it 1.369 r_mcbond_it 0.813 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.207 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.496 r_scangle_it 4.162 r_scbond_it 2.554 r_angle_refined_deg 1.497 r_mcangle_it 1.369 r_mcbond_it 0.813 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.207 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.112 r_metal_ion_refined 0.029 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3286 Nucleic Acid Atoms Solvent Atoms 787 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing