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Structural basis for ion-coordination and the catalytic mechanism of sphingomyelinases D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.818 α = 90 b = 139.818 β = 90 c = 113.461 γ = 120
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 MARRESEARCH 2004-08-09 M SINGLE WAVELENGTH 2 1 100 IMAGE PLATE MARRESEARCH osmic mirrors 2004-08-20
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.427 LNLS D03B-MX1 2 ROTATING ANODE OTHER
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 1.75 30 99.5 0.057 22 20.5 125875
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) 1.75 1.79 99.5 0.305 3.4 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SIRAS THROUGHOUT 1.75 30 119510 6315 99.51 0.198 0.18761 0.18566 0.1843 0.22465 0.2232 RANDOM 24.248
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] 0.04 0.02 0.04 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.728 r_dihedral_angle_3_deg 14.564 r_dihedral_angle_4_deg 14.26 r_dihedral_angle_1_deg 6.53 r_scangle_it 3.37 r_scbond_it 2.308 r_mcangle_it 1.634 r_angle_refined_deg 1.551 r_mcbond_it 0.955 r_nbtor_refined 0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.728 r_dihedral_angle_3_deg 14.564 r_dihedral_angle_4_deg 14.26 r_dihedral_angle_1_deg 6.53 r_scangle_it 3.37 r_scbond_it 2.308 r_mcangle_it 1.634 r_angle_refined_deg 1.551 r_mcbond_it 0.955 r_nbtor_refined 0.328 r_nbd_refined 0.222 r_symmetry_hbond_refined 0.211 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.122 r_metal_ion_refined 0.066 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9076 Nucleic Acid Atoms Solvent Atoms 1018 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling SHELXS phasing