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Crystal structure of the HsaC extradiol dioxygenase from M. tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KND PDB ENTRY 1KND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 298 pH 6.80, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.04 59.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.737 α = 90 b = 123.737 β = 90 c = 106.784 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 100 IMAGE PLATE MAR scanner 345 mm plate 2006-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.541
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 26 99.9 0.094 0.091 7.7 14 56597 56445 1 21.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.2 99.9 0.458 0.441 1.6 13.4
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 (All) 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 1KND 2 20 53592 53536 2861 100 0.18 0.182 0.18 0.1861 0.223 0.1852 RANDOM 19.41
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] -0.53 -0.53 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.827 r_dihedral_angle_4_deg 17.957 r_dihedral_angle_3_deg 16.146 r_dihedral_angle_1_deg 10.497 r_angle_refined_deg 1.673 r_mcangle_it 1.344 r_mcbond_it 0.893 r_nbtor_refined 0.298 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.827 r_dihedral_angle_4_deg 17.957 r_dihedral_angle_3_deg 16.146 r_dihedral_angle_1_deg 10.497 r_angle_refined_deg 1.673 r_mcangle_it 1.344 r_mcbond_it 0.893 r_nbtor_refined 0.298 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.197 r_xyhbond_nbd_refined 0.176 r_symmetry_hbond_refined 0.169 r_chiral_restr 0.132 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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_scbond_it 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 4677 Nucleic Acid Atoms Solvent Atoms 675 Heterogen Atoms 12
Software Software Software Name Purpose PHASER phasing REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling