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Crystal structure of human acyl-CoA synthetase medium-chain family member 2A, with L64P mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PG3 PDB entry 1PG3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M HEPES pH 7.5, 1.4M Na citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.75 67.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.426 α = 90 b = 109.173 β = 90 c = 176.926 γ = 90
Symmetry Space Group I 2 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 IMAGE PLATE RIGAKU RAXIS HTC OSMIC MIRRORS 2007-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 50.57 98.9 0.077 0.04 12.8 4.6 63810 60580 2.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 98.2 0.872 0.446 2 4.7
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 PDB entry 1PG3 2 50 60580 60580 3225 98.81 0.17136 0.16903 0.169 0.21385 0.2073 RANDOM 28.86
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] -1.85 0.8 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.624 r_dihedral_angle_4_deg 16.409 r_dihedral_angle_3_deg 13.089 r_scangle_it 9.204 r_scbond_it 7.72 r_dihedral_angle_1_deg 6.089 r_mcangle_it 4.599 r_mcbond_it 3.823 r_angle_refined_deg 1.446 r_mcbond_other 1.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.624 r_dihedral_angle_4_deg 16.409 r_dihedral_angle_3_deg 13.089 r_scangle_it 9.204 r_scbond_it 7.72 r_dihedral_angle_1_deg 6.089 r_mcangle_it 4.599 r_mcbond_it 3.823 r_angle_refined_deg 1.446 r_mcbond_other 1.159 r_angle_other_deg 0.939 r_nbd_refined 0.198 r_symmetry_vdw_other 0.198 r_nbd_other 0.195 r_nbtor_refined 0.173 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.161 r_symmetry_vdw_refined 0.092 r_nbtor_other 0.088 r_chiral_restr 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4126 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling PHASER phasing