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Crystal structure of ketol-acid reductoisomerase from Azotobacter
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NP3 PDB entry 1NP3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 0.25 M NaCl, 28 % PEG3350 and 0.1 M Bis-Tris, pH 5.5, strictly anaerobic
Crystal Properties Matthews coefficient Solvent content 3.6 65.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.05 α = 90 b = 185.05 β = 90 c = 185.05 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2012-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000, 1.7448 SLS X06SA
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 2.5 82.76 99.5 0.092 10.9 3.5 72509
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 2.5 2.64 99.9 0.513 2.6 3.6
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 1NP3 2.5 55.79 68666 3656 99.2 0.19646 0.19392 0.1991 0.24377 0.245 RANDOM 47.799
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]
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 8.146 r_long_range_B_other 8.146 r_scangle_other 6.203 r_mcangle_it 5.639 r_mcangle_other 5.639 r_scbond_it 3.963 r_scbond_other 3.963 r_mcbond_it 3.771 r_mcbond_other 3.767 r_angle_refined_deg 1.72
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 8.146 r_long_range_B_other 8.146 r_scangle_other 6.203 r_mcangle_it 5.639 r_mcangle_other 5.639 r_scbond_it 3.963 r_scbond_other 3.963 r_mcbond_it 3.771 r_mcbond_other 3.767 r_angle_refined_deg 1.72 r_angle_other_deg 1.655 r_chiral_restr 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9964 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing SHELX phasing