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Crystal Structure Analysis of GM2-activator protein complexed with phosphatidylcholine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PU5 1PU5 monomer B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 278 Peg 4000, Hepes buffer, isopropanol, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 3.02 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.5 α = 90 b = 64.09 β = 92.81 c = 80.99 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 123 CCD MAR CCD 165 mm 2003-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97943 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 1.6 28 93.8 0.043 22 3.4 56004 52552 1 1 21.5
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 1.6 1.66 89.7 0.315 3.9 3.3 5632
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1PU5 monomer B 1.8 19.85 1 37646 3099 95.4 0.188 0.188 0.1882 0.224 0.224 RANDOM 26.7
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] -0.38 -1.81 -0.97 1.35
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.1 c_scbond_it 12.17 c_scangle_it 6.99 c_mcangle_it 3.44 c_mcbond_it 2.36 c_angle_deg 1.5 c_improper_angle_d 1.12 c_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2496 Nucleic Acid Atoms Solvent Atoms 639 Heterogen Atoms 158
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing