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Structure and protein design of human apyrase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S18 PDB ENTRY 1S18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 295 PEG MME 2000, sodium acetate, ammonium sulfate, strontium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.24 44.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.163 α = 98.99 b = 52.45 β = 106.99 c = 77.478 γ = 100.09
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 2003-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.98 NSLS X4A
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 1.6 46.6 95 0.059 12 1.9 79084 79084 16.4
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) 1.6 1.66 93.8 0.348 2.3 1.9 7743
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 PDB ENTRY 1S18 1.6 46.6 79084 75102 3982 95 0.16581 0.16581 0.16427 0.1653 0.19399 0.1942 RANDOM 18.372
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] -0.35 0.24 -0.07 -0.07 -0.37 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.663 r_scangle_it 4.275 r_scbond_it 2.66 r_mcangle_it 1.747 r_angle_refined_deg 1.543 r_mcbond_it 0.975 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.192 r_symmetry_vdw_refined 0.167 r_metal_ion_refined 0.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.663 r_scangle_it 4.275 r_scbond_it 2.66 r_mcangle_it 1.747 r_angle_refined_deg 1.543 r_mcbond_it 0.975 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.192 r_symmetry_vdw_refined 0.167 r_metal_ion_refined 0.157 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4998 Nucleic Acid Atoms Solvent Atoms 650 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing