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Crystal structure of Bacillus cereus sphingomyelinase mutant :N57A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DDT PDB ENTRY 2DDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1 M CALCIUM ACETATE 0.2 M SODIUM CACODYLATE (PH7.5) 18% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.63 53.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.09 α = 90 b = 63.927 β = 90 c = 101.69 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 RIGAKU IMAGING PLATE MIRRORS 2006-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E
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 48.44 98.7 0.15 4.9 11.2 14493 1
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 2.4 2.49 96.5 0.33
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2DDT 2.4 54.15 13721 724 98.6 0.184 0.182 0.1775 0.235 RANDOM 27.52
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] 0.77 -0.08 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.539 r_dihedral_angle_4_deg 19.305 r_dihedral_angle_3_deg 17.718 r_dihedral_angle_1_deg 7.175 r_scangle_it 4.141 r_scbond_it 2.71 r_mcangle_it 2.046 r_angle_refined_deg 1.631 r_mcbond_it 1.139 r_angle_other_deg 0.761
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.539 r_dihedral_angle_4_deg 19.305 r_dihedral_angle_3_deg 17.718 r_dihedral_angle_1_deg 7.175 r_scangle_it 4.141 r_scbond_it 2.71 r_mcangle_it 2.046 r_angle_refined_deg 1.631 r_mcbond_it 1.139 r_angle_other_deg 0.761 r_symmetry_hbond_refined 0.356 r_nbtor_refined 0.306 r_nbtor_other 0.274 r_nbd_other 0.228 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.121 r_mcbond_other 0.106 r_bond_other_d 0.059 r_metal_ion_refined 0.023 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2361 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CCP4I phasing