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Native AphA class B acid phosphatase/phosphotransferase from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B82 PDB entry 2B82
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 279 drop: 4.2-3.5 mg/mL in 50 mM CH3COONa buffer at pH 7.2, 10 mM MgCl2
reservoir:
18% (w/v) polyethylene glycol (PEG) 6000, 0.6% (w/v) Spermine, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 3.34 63.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.294 α = 90 b = 92.775 β = 90 c = 137.6 γ = 90
Symmetry Space Group I 2 2 2
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 Monochromator double crystal, Si(111); toroidal mirror 2002-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.934 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 8 96.8 0.092 4.4 4.3 31967 2 17.14
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) 1.7 1.742 99.51 0.165 0.165 2.3 4.14 2311
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 PDB entry 2B82 1.7 7.99 2 31967 31967 1717 96.84 0.181 0.181 0.181 0.1806 0.21167 0.2115 RANDOM 23.54
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.098 r_dihedral_angle_4_deg 18.695 r_dihedral_angle_3_deg 12.224 r_dihedral_angle_1_deg 4.99 r_scangle_it 2.86 r_scbond_it 1.79 r_mcangle_it 1.176 r_angle_refined_deg 1.082 r_mcbond_it 0.692 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.098 r_dihedral_angle_4_deg 18.695 r_dihedral_angle_3_deg 12.224 r_dihedral_angle_1_deg 4.99 r_scangle_it 2.86 r_scbond_it 1.79 r_mcangle_it 1.176 r_angle_refined_deg 1.082 r_mcbond_it 0.692 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.231 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.111 r_chiral_restr 0.084 r_metal_ion_refined 0.021 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1680 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling MOLREP phasing