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Crystal structure of the E130Y mutant of human soluble calcium-activated nucleotidase (SCAN) with calcium ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 293 16% PEG 4000, 0.2 M ammonium sulfate, 0.1M sodium acetate pH4.8, 10 mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.12 41.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.891 α = 100.94 b = 52.412 β = 106.51 c = 77.806 γ = 99.32
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 MARMOSAIC 300 mm CCD 2006-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97182 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.4 50 86.8 0.065 18.4 1.7 20989
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.49 83.8 0.451 1.5 2060
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1S1D 2.4 47.04 20960 1075 86.45 0.22 0.22 0.216 0.2166 0.285 0.2871 RANDOM 46.135
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] 0.02 -0.01 0.02 0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.81 r_dihedral_angle_3_deg 20.257 r_dihedral_angle_4_deg 16.511 r_dihedral_angle_1_deg 7.524 r_scangle_it 2.305 r_angle_refined_deg 1.48 r_scbond_it 1.465 r_mcangle_it 1.285 r_mcbond_it 0.726 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.81 r_dihedral_angle_3_deg 20.257 r_dihedral_angle_4_deg 16.511 r_dihedral_angle_1_deg 7.524 r_scangle_it 2.305 r_angle_refined_deg 1.48 r_scbond_it 1.465 r_mcangle_it 1.285 r_mcbond_it 0.726 r_nbtor_refined 0.313 r_symmetry_hbond_refined 0.306 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.1 r_metal_ion_refined 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5004 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection