☰ Navigation Tabs
Crystal structure of the M. tuberculosis sulfate ester dioxygenase Rv3406 in complex with iron.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FFA PDB ENTRY 4FFA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 22% PEG2000, 300 MM MAGNESIUM NITRATE, 100 MM TRIS/HCL PH 8.0, 2% MPD
Crystal Properties Matthews coefficient Solvent content 2.18 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.97 α = 90 b = 128.15 β = 90 c = 138.42 γ = 90
Symmetry Space Group P 21 21 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 PIXEL PILATUS 2013-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 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 43.4 98 0.12 8.2 4.7 74877 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.04
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 4FFA 2 94.04 71028 3773 97.8 0.21 0.20765 0.2167 0.25382 0.259 RANDOM 39.837
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] 5.41 -2.73 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.537 r_dihedral_angle_3_deg 16.675 r_dihedral_angle_4_deg 16.355 r_dihedral_angle_1_deg 7.151 r_mcangle_it 4.292 r_scbond_it 3.769 r_mcbond_it 3.058 r_mcbond_other 3.046 r_angle_refined_deg 1.741 r_angle_other_deg 0.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.537 r_dihedral_angle_3_deg 16.675 r_dihedral_angle_4_deg 16.355 r_dihedral_angle_1_deg 7.151 r_mcangle_it 4.292 r_scbond_it 3.769 r_mcbond_it 3.058 r_mcbond_other 3.046 r_angle_refined_deg 1.741 r_angle_other_deg 0.877 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it 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 7466 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling BALBES phasing