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Crystal structure of a fragment of rat phospholipase Cepsilon EF3-RA1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OHM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 285.15 6.25% PEG 4000, 100 mM MES pH 6.00, 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.21 44.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.572 α = 90 b = 127.755 β = 101.12 c = 139.337 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 110 PIXEL DECTRIS PILATUS3 6M 2018-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03 APS 23-ID-D
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 2.73 136.72 99.6 0.268 0.319 0.171 0.971 5.1 3.4 84933
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 2.73 2.88 99.7 1.794 2.12 1.122 0.334 3.5
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 3OHM 2.73 20 80469 4196 99.27 0.23591 0.23397 0.2357 0.27278 0.273 RANDOM 58.286
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] -0.6 -0.12 -0.21 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.789 r_dihedral_angle_3_deg 19.656 r_dihedral_angle_4_deg 16.928 r_dihedral_angle_1_deg 7.843 r_long_range_B_refined 3.329 r_long_range_B_other 3.329 r_mcangle_it 2.007 r_mcangle_other 2.007 r_scangle_other 1.867 r_angle_refined_deg 1.714
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.789 r_dihedral_angle_3_deg 19.656 r_dihedral_angle_4_deg 16.928 r_dihedral_angle_1_deg 7.843 r_long_range_B_refined 3.329 r_long_range_B_other 3.329 r_mcangle_it 2.007 r_mcangle_other 2.007 r_scangle_other 1.867 r_angle_refined_deg 1.714 r_angle_other_deg 1.253 r_mcbond_it 1.157 r_mcbond_other 1.157 r_scbond_it 1.073 r_scbond_other 1.073 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19622 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction DIALS data reduction PHASER phasing