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Crystal structure of D48V mutant of human GLTP bound with 12:0 monosulfatide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S0I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 15% PEG 3350, 0.1M MES pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.95 37.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.984 α = 90 b = 47.242 β = 125.52 c = 62.193 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 2009-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9754 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.35 50 99.8 69954 40558 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.4 99.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3S0I 1.35 15 2 40407 38442 1965 99.79 0.15359 0.15359 0.15215 0.1553 0.18078 0.1528 RANDOM 20.404
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] -0.82 -0.48 -0.08 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.025 r_dihedral_angle_3_deg 12.468 r_dihedral_angle_4_deg 11.354 r_sphericity_free 5.786 r_dihedral_angle_1_deg 5.426 r_scangle_it 4.229 r_sphericity_bonded 4.128 r_scbond_it 3.333 r_mcangle_it 2.25 r_mcbond_it 1.911
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.025 r_dihedral_angle_3_deg 12.468 r_dihedral_angle_4_deg 11.354 r_sphericity_free 5.786 r_dihedral_angle_1_deg 5.426 r_scangle_it 4.229 r_sphericity_bonded 4.128 r_scbond_it 3.333 r_mcangle_it 2.25 r_mcbond_it 1.911 r_rigid_bond_restr 1.839 r_angle_refined_deg 1.602 r_angle_other_deg 1.273 r_mcbond_other 0.729 r_symmetry_vdw_other 0.32 r_symmetry_hbond_refined 0.233 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.212 r_nbtor_refined 0.192 r_nbd_other 0.177 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.094 r_nbtor_other 0.088 r_xyhbond_nbd_other 0.043 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1611 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 64
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling