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Crystal Structure of D48V mutant of Human Glycolipid Transfer Protein complexed with 3-O-sulfo galactosylceramide containing nervonoyl acyl chain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RZN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 273 20-25% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.01 38.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.315 α = 90 b = 47.454 β = 125.47 c = 63.257 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 2009-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.5 30 99.9 0.061 8.8 5.1 30330 2
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 1.5 1.55 99.9 0.444 2 3.2
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 (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 3RZN 1.5 15 30330 28748 1469 99.53 0.15648 0.15408 0.1507 0.20599 0.2034 RANDOM 29.447
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] -0.11 -0.09 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.364 r_sphericity_free 27.668 r_sphericity_bonded 16.513 r_dihedral_angle_3_deg 14.264 r_dihedral_angle_4_deg 13.73 r_dihedral_angle_1_deg 4.872 r_scangle_it 4.429 r_scbond_it 3.502 r_rigid_bond_restr 3.211 r_mcangle_it 2.435
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.364 r_sphericity_free 27.668 r_sphericity_bonded 16.513 r_dihedral_angle_3_deg 14.264 r_dihedral_angle_4_deg 13.73 r_dihedral_angle_1_deg 4.872 r_scangle_it 4.429 r_scbond_it 3.502 r_rigid_bond_restr 3.211 r_mcangle_it 2.435 r_mcbond_it 2.108 r_angle_refined_deg 1.294 r_mcbond_other 0.847 r_symmetry_vdw_refined 0.298 r_symmetry_hbond_refined 0.28 r_symmetry_vdw_other 0.261 r_nbd_refined 0.24 r_nbd_other 0.193 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.168 r_nbtor_other 0.092 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.001 r_bond_other_d r_angle_other_deg r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1618 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 61
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling