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Crystal structure of human acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in complex with AMP-CPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C5E PDB entry 3C5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 25% PEG 3350, 0.20M NaCl, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.59 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.508 α = 90 b = 97.835 β = 90 c = 120.415 γ = 90
Symmetry Space Group P 21 21 21
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 2008-03-17 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 1.95 32.72 98.2 0.089 0.055 11 3.5 48550 45963 2
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 1.95 2.06 93.4 0.491 0.303 2.3 3.3 6604
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 3C5E 1.95 31.51 45963 45963 2441 97.88 0.16398 0.16398 0.16095 0.1715 0.22033 0.2285 RANDOM 13.974
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] -0.26 -0.55 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.695 r_dihedral_angle_4_deg 17.191 r_dihedral_angle_3_deg 13.532 r_scangle_it 8.845 r_scbond_it 6.747 r_dihedral_angle_1_deg 6.312 r_mcangle_it 4.216 r_mcbond_it 3.048 r_angle_refined_deg 1.555 r_mcbond_other 1.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.695 r_dihedral_angle_4_deg 17.191 r_dihedral_angle_3_deg 13.532 r_scangle_it 8.845 r_scbond_it 6.747 r_dihedral_angle_1_deg 6.312 r_mcangle_it 4.216 r_mcbond_it 3.048 r_angle_refined_deg 1.555 r_mcbond_other 1.031 r_angle_other_deg 0.989 r_chiral_restr 0.094 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 4150 Nucleic Acid Atoms Solvent Atoms 763 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling PHASER phasing