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Human StarD13 (DLC2) lipid transfer and protein localization domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JSS PDB entry 1JSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 20 % MPD, 100 mM Tris-HCl, 125 mM NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.08 69.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.24 α = 90 b = 78.24 β = 90 c = 212.72 γ = 90
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 ADSC QUANTUM 315 mirrors 2006-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 1.03992 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.8 20 99.5 0.073 16.69 7.5 31213 31213 86.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 100 0.554 3.52 7.6 3157
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 1JSS 2.8 19.79 29640 29640 1572 99.77 0.2115 0.2115 0.20973 0.2064 0.24446 0.2425 RANDOM 45.487
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.424 r_dihedral_angle_3_deg 20.139 r_dihedral_angle_4_deg 18.411 r_dihedral_angle_1_deg 7.333 r_mcangle_it 3.943 r_scangle_it 3.361 r_mcbond_it 2.406 r_scbond_it 2.214 r_angle_refined_deg 1.454 r_nbtor_refined 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.424 r_dihedral_angle_3_deg 20.139 r_dihedral_angle_4_deg 18.411 r_dihedral_angle_1_deg 7.333 r_mcangle_it 3.943 r_scangle_it 3.361 r_mcbond_it 2.406 r_scbond_it 2.214 r_angle_refined_deg 1.454 r_nbtor_refined 0.332 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.197 r_xyhbond_nbd_refined 0.169 r_symmetry_vdw_refined 0.15 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4477 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ProDC data collection XDS data reduction XSCALE data scaling PHASER phasing MOLREP phasing