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Crystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex with adenosine and phosphate at 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 7.2 298 AphA 6mg/mL, 50 mM Na acetate, 25% PEG 6000, 10mM AMP, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.966 α = 90 b = 66.544 β = 124.02 c = 91.544 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 monochromator 2003-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.001 ELETTRA 5.2R
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 2.033 49.65 97.4 0.077 0.077 6.2 3 28127 28127 19.44
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 2.033 2.14 89.6 0.147 0.147 4.2 2.5 3767
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1N8N 2.033 49.39 25795 25795 2330 100 0.17545 0.17545 0.17123 0.22258 0.2222 RANDOM 18.581
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 -0.84 -0.75 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.108 r_dihedral_angle_4_deg 16.857 r_dihedral_angle_3_deg 14.273 r_dihedral_angle_1_deg 6.162 r_scangle_it 4.117 r_scbond_it 2.578 r_angle_refined_deg 1.591 r_mcangle_it 1.56 r_mcbond_it 0.869 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.108 r_dihedral_angle_4_deg 16.857 r_dihedral_angle_3_deg 14.273 r_dihedral_angle_1_deg 6.162 r_scangle_it 4.117 r_scbond_it 2.578 r_angle_refined_deg 1.591 r_mcangle_it 1.56 r_mcbond_it 0.869 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.222 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_metal_ion_refined 0.009 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 3314 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 42
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling