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Crystal structure of human acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in complex with AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B7W PDB ENTRY 3B7W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2M AMMONIUM ACETATE, 0.1M TRIS PH 8.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.42 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.73 α = 90 b = 97.73 β = 90 c = 384.6 γ = 90
Symmetry Space Group P 41 21 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 RIGAKU AREA DETECTOR OSMIC 2008-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT
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 2.45 37.99 98.1 0.01 9.58 3 73402 2
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 2.45 2.71 97.1 0.49 2 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3B7W 2.45 39.16 65612 3454 100 0.196 0.193 0.2082 0.243 0.2552 RANDOM 1.86
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] -0.04 -0.04 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.146 r_dihedral_angle_4_deg 15.28 r_dihedral_angle_3_deg 14.966 r_dihedral_angle_1_deg 5.821 r_scangle_it 2.581 r_scbond_it 1.951 r_angle_refined_deg 1.452 r_angle_other_deg 0.919 r_mcangle_it 0.596 r_mcbond_it 0.381
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.146 r_dihedral_angle_4_deg 15.28 r_dihedral_angle_3_deg 14.966 r_dihedral_angle_1_deg 5.821 r_scangle_it 2.581 r_scbond_it 1.951 r_angle_refined_deg 1.452 r_angle_other_deg 0.919 r_mcangle_it 0.596 r_mcbond_it 0.381 r_symmetry_hbond_refined 0.217 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.21 r_nbd_other 0.198 r_symmetry_vdw_other 0.194 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.112 r_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12382 Nucleic Acid Atoms Solvent Atoms 655 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing