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Crystal structure of SEC14-like protein 4 (SEC14L4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2M Magnesium Chloride -- 0.1M tris pH 8.5 -- 25%(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.6 52.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.185 α = 90 b = 79.495 β = 95.18 c = 82.395 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 100 PIXEL PSI PILATUS 6M 2013-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.92 Diamond I04
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 1.77 37.33 95.5 0.089 17.2 7.3 640884 18.4
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 1OLM 1.77 37.33 83615 4425 95.39 0.14118 0.13843 0.1513 0.19425 0.2024 RANDOM 27.583
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] -0.57 -0.22 -0.08 0.68
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.531 r_dihedral_angle_2_deg 32.935 r_dihedral_angle_4_deg 17.019 r_sphericity_bonded 16.857 r_dihedral_angle_3_deg 11.619 r_long_range_B_refined 5.704 r_long_range_B_other 5.704 r_dihedral_angle_1_deg 5.549 r_scangle_other 5.209 r_mcangle_it 4.457
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.531 r_dihedral_angle_2_deg 32.935 r_dihedral_angle_4_deg 17.019 r_sphericity_bonded 16.857 r_dihedral_angle_3_deg 11.619 r_long_range_B_refined 5.704 r_long_range_B_other 5.704 r_dihedral_angle_1_deg 5.549 r_scangle_other 5.209 r_mcangle_it 4.457 r_mcangle_other 4.457 r_scbond_it 4.33 r_scbond_other 4.33 r_mcbond_it 3.683 r_mcbond_other 3.682 r_rigid_bond_restr 2.411 r_angle_refined_deg 1.286 r_angle_other_deg 0.803 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6182 Nucleic Acid Atoms Solvent Atoms 461 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement