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The X-ray Structure of Chlorobium vibrioforme 5-Aminolaevulinic Acid Dehydratase Complexed with a Diacid Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W1Z PDB ENTRY 1W1Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.23 44.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.48 α = 90 b = 126.48 β = 90 c = 81.85 γ = 90
Symmetry Space Group P 4 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 30 CCD ADSC CCD 2004-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.6 89 91.6 0.12 5.6 4 24586
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 2.6 2.74 94.1 0.49 1.6 4
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1W1Z 2.6 89.44 17930 980 90 0.263 0.26 0.32 RANDOM 36.05
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] -0.29 -0.29 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.461 r_dihedral_angle_4_deg 19.082 r_dihedral_angle_3_deg 18.524 r_dihedral_angle_1_deg 4.882 r_scangle_it 1.201 r_angle_refined_deg 1.034 r_scbond_it 0.723 r_mcangle_it 0.57 r_mcbond_it 0.357 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.461 r_dihedral_angle_4_deg 19.082 r_dihedral_angle_3_deg 18.524 r_dihedral_angle_1_deg 4.882 r_scangle_it 1.201 r_angle_refined_deg 1.034 r_scbond_it 0.723 r_mcangle_it 0.57 r_mcbond_it 0.357 r_nbtor_refined 0.298 r_xyhbond_nbd_refined 0.283 r_symmetry_hbond_refined 0.207 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.181 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 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_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 4962 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing