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X-ray structure of human alkaline phosphatase in complex with strontium
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 Crystals were grown at 19 (2) using sitting drop vapor diffusion, with protein concentration of 10mg/ml, in the presence of 10mM p-nitrophenyl phosphate. Crystals were obtained from 12% PEG 3350, 100mM sodium cacodylate pH 6.5, 1mM zinc chloride, 2mM magnesium acetate, and 2mM strontium chloride over a period of five months, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.09 α = 90 b = 115.299 β = 90 c = 107.32 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.6 100 99 0.096 19.25 72276 72276
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.65 96.9 0.431 2.88
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 1.6 9.99 71854 68217 3637 99 0.14991 0.14991 0.14778 0.18813 0.1928 RANDOM 17.399
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] -0.03 0.1 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.904 r_scangle_it 4.373 r_sphericity_free 3.354 r_scbond_it 2.869 r_sphericity_bonded 2.116 r_mcangle_it 1.884 r_angle_refined_deg 1.751 r_rigid_bond_restr 1.599 r_mcbond_it 1.184 r_angle_other_deg 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.904 r_scangle_it 4.373 r_sphericity_free 3.354 r_scbond_it 2.869 r_sphericity_bonded 2.116 r_mcangle_it 1.884 r_angle_refined_deg 1.751 r_rigid_bond_restr 1.599 r_mcbond_it 1.184 r_angle_other_deg 1.02 r_symmetry_vdw_other 0.301 r_nbd_refined 0.263 r_nbd_other 0.258 r_symmetry_hbond_refined 0.251 r_xyhbond_nbd_refined 0.215 r_symmetry_vdw_refined 0.161 r_chiral_restr 0.145 r_metal_ion_refined 0.127 r_nbtor_other 0.088 r_bond_refined_d 0.017 r_gen_planes_other 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3660 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data scaling