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Crystal Structure of the Biotin Carboxylase Subunit, E23R mutant, of Acetyl-CoA Carboxylase from Escherichia coli.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DV1 PDB ENTRY 1DV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 294 0.1 M magnesium formate, 14% (w/v) PEG3350, 8% (v/v) glycerol, and 20 mM calcium chloride, pH 8.5, VAPOR DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.49 50.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.926 α = 90 b = 92.619 β = 98.84 c = 86.598 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 100 CCD ADSC QUANTUM 4 2005-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97924 NSLS X4A
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 2.8 30 97.7 0.064 16.1503 3 24249 23691 -3 -3
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 2.8 2.9 90.7 0.3 3.131 2.6
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 1DV1 2.8 30 22813 21174 1639 93.67 0.20551 0.2013 0.2033 0.25979 0.2218 RANDOM 45.208
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] -3.26 -0.06 4.55 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.957 r_dihedral_angle_4_deg 19.201 r_dihedral_angle_3_deg 18.409 r_dihedral_angle_1_deg 5.629 r_scangle_it 2.389 r_angle_refined_deg 1.468 r_scbond_it 1.437 r_mcangle_it 1.196 r_mcbond_it 0.679 r_symmetry_hbond_refined 0.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.957 r_dihedral_angle_4_deg 19.201 r_dihedral_angle_3_deg 18.409 r_dihedral_angle_1_deg 5.629 r_scangle_it 2.389 r_angle_refined_deg 1.468 r_scbond_it 1.437 r_mcangle_it 1.196 r_mcbond_it 0.679 r_symmetry_hbond_refined 0.359 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.306 r_nbd_refined 0.245 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6896 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling COMO phasing