☰ Navigation Tabs
Crystal structure of D48V mutant of human GLTP bound with 12:0 disulfatide (hexagonal form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 10-20% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.8 56.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.019 α = 90 b = 111.019 β = 90 c = 75.206 γ = 120
Symmetry Space Group P 64 2 2
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 2009-04-13 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 2.9 50 96.5 6872 6872 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 2.9 3.02 95.6
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 4H2Z 2.9 14.81 1 6182 5877 297 96.82 0.19771 0.19771 0.19322 0.2296 0.28201 0.2031 RANDOM 54.335
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 -0.06 -0.11 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.347 r_dihedral_angle_3_deg 21.088 r_dihedral_angle_4_deg 12.645 r_dihedral_angle_1_deg 6.972 r_scangle_it 2.358 r_angle_refined_deg 1.713 r_scbond_it 1.463 r_mcangle_it 1.011 r_angle_other_deg 0.956 r_mcbond_it 0.849
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.347 r_dihedral_angle_3_deg 21.088 r_dihedral_angle_4_deg 12.645 r_dihedral_angle_1_deg 6.972 r_scangle_it 2.358 r_angle_refined_deg 1.713 r_scbond_it 1.463 r_mcangle_it 1.011 r_angle_other_deg 0.956 r_mcbond_it 0.849 r_nbd_refined 0.248 r_nbtor_refined 0.204 r_nbd_other 0.192 r_symmetry_vdw_other 0.175 r_xyhbond_nbd_refined 0.158 r_symmetry_vdw_refined 0.148 r_symmetry_hbond_refined 0.11 r_mcbond_other 0.094 r_nbtor_other 0.093 r_chiral_restr 0.087 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1659 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 53
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling