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Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ion
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 283 18% (w/v) PEG 8000, 0.2M magnesium sulfate, 0.1mM calcium chrolide, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.17 43.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.844 α = 81.87 b = 50.893 β = 81.84 c = 59.506 γ = 79.68
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 RIGAKU JUPITER 2004-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.000 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 50 90.8 48543 48543
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.9 93
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 (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 1.8 49.69 48541 48541 2438 90.77 0.19478 0.19295 0.2017 0.23024 0.241 RANDOM 19.288
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 0.4 0.76 -0.25 0.66 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.418 r_dihedral_angle_4_deg 16.469 r_dihedral_angle_3_deg 10.911 r_scangle_it 3.998 r_angle_other_deg 3.637 r_scbond_it 3.221 r_angle_refined_deg 2.161 r_mcangle_it 2.062 r_dihedral_angle_1_deg 2.014 r_mcbond_it 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.418 r_dihedral_angle_4_deg 16.469 r_dihedral_angle_3_deg 10.911 r_scangle_it 3.998 r_angle_other_deg 3.637 r_scbond_it 3.221 r_angle_refined_deg 2.161 r_mcangle_it 2.062 r_dihedral_angle_1_deg 2.014 r_mcbond_it 1.82 r_mcbond_other 0.392 r_symmetry_vdw_refined 0.293 r_chiral_restr 0.268 r_symmetry_vdw_other 0.263 r_nbd_other 0.246 r_nbd_refined 0.212 r_nbtor_refined 0.191 r_symmetry_hbond_refined 0.167 r_xyhbond_nbd_refined 0.122 r_nbtor_other 0.112 r_xyhbond_nbd_other 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4570 Nucleic Acid Atoms Solvent Atoms 534 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing