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Crystal structure of D48V mutant of human Glycolipid Transfer Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SWX PDB ENTRY 1SWX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 PEG, potassium phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.459 α = 90 b = 35.36 β = 116.47 c = 58.011 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 293 IMAGE PLATE RIGAKU RAXIS HTC mirrors 2004-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 1.99 20 98.1 0.104 18.7 3.5 13588 13588
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 1.99 2.07 94.6 0.498 3.4 1298
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 1SWX 1.99 20 13588 13587 678 97.27 0.203 0.203 0.201 0.2066 0.255 0.2588 RANDOM 30.389
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] 0.06 0.33 -1.21 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.258 r_scangle_it 2.594 r_scbond_it 1.487 r_angle_other_deg 1.171 r_angle_refined_deg 1.12 r_mcangle_it 1.041 r_mcbond_it 0.534 r_symmetry_hbond_refined 0.225 r_nbd_other 0.22 r_symmetry_vdw_other 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.258 r_scangle_it 2.594 r_scbond_it 1.487 r_angle_other_deg 1.171 r_angle_refined_deg 1.12 r_mcangle_it 1.041 r_mcbond_it 0.534 r_symmetry_hbond_refined 0.225 r_nbd_other 0.22 r_symmetry_vdw_other 0.22 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.162 r_nbtor_other 0.098 r_chiral_restr 0.056 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1619 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction AMoRE phasing