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crystal structure of human peroxisomal delta3,5,delta2,4-dienoyl coa isomerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DCI PDB ENTRY 1DCI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2M CA(AC)2, 0.1M CACODYLATE PH 6.5, 18% PEG 8K
Crystal Properties Matthews coefficient Solvent content 2.31 46.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.58 α = 90 b = 137.253 β = 90 c = 96.137 γ = 90
Symmetry Space Group C 2 2 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 CCD MARRESEARCH 2008-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.95 93.25 99.8 0.08 10.3 3.7 58508
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 1.95 2 100 0.63 2 3.7
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 1DCI 1.95 93.25 58508 3132 100 0.169 0.167 0.1853 0.202 0.2127 RANDOM 37.71
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] -0.96 -0.29 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.188 r_dihedral_angle_4_deg 15.276 r_dihedral_angle_3_deg 14.115 r_scangle_it 6.799 r_dihedral_angle_1_deg 6.104 r_scbond_it 4.711 r_mcangle_it 2.641 r_mcbond_it 1.706 r_angle_refined_deg 1.348 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.188 r_dihedral_angle_4_deg 15.276 r_dihedral_angle_3_deg 14.115 r_scangle_it 6.799 r_dihedral_angle_1_deg 6.104 r_scbond_it 4.711 r_mcangle_it 2.641 r_mcbond_it 1.706 r_angle_refined_deg 1.348 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_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 6005 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing