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Crystal structure of human alkaline ceramidase 3 (ACER3) at 2.7 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RWD 4RWD plus fragments derived from an I-TASSER ab-initio model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 7.5 293.15 75mM MgSO4, 34-40% PEG400, 5% DMSO
Crystal Properties Matthews coefficient Solvent content 3.33 63.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.88 α = 90 b = 68.83 β = 90 c = 257.52 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS EIGER X 16M 2017-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00001 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.7 45.6 100 0.566 0.577 0.11 0.964 8.1 27.6 15327 64.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 100 4.491 4.575 0.865 0.496 27.7
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4RWD plus fragments derived from an I-TASSER ab-initio model 2.7 45.6 15325 716 100 0.249 0.248 0.2589 0.27 0.2627 RANDOM 74.44
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] -14.1731 1.798 12.3752
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.3 t_omega_torsion 2.06 t_angle_deg 0.97 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.3 t_omega_torsion 2.06 t_angle_deg 0.97 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2855 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 62
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction