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Crystal structure of naphthalene 1,2-dioxygenase from Rhodococcus sp. bound to indole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B1X PDB ENTRY 2B1X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 279 0.1 M HEPES, PH 7.8, 68% MPD, 40 MG/ML PROTEIN, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 4.54 72.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.358 α = 90 b = 179.358 β = 90 c = 245.411 γ = 90
Symmetry Space Group P 43 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 CCD ADSC QUANTUM 210 2002-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00 APS 17-ID
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 3 20.42 99.2 0.116 12.3 5.8 79677 79677
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 3 3.11 98.6 0.265 5.4 4.16
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 2B1X 3 20.42 77193 77193 2397 99.28 0.28728 0.28728 0.28688 0.2647 0.29992 0.2764 RANDOM 92.273
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] 0.8 0.8 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.415 r_scangle_it 1.919 r_angle_refined_deg 1.391 r_mcangle_it 1.1 r_scbond_it 1.099 r_mcbond_it 0.587 r_symmetry_vdw_refined 0.303 r_symmetry_hbond_refined 0.235 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.415 r_scangle_it 1.919 r_angle_refined_deg 1.391 r_mcangle_it 1.1 r_scbond_it 1.099 r_mcbond_it 0.587 r_symmetry_vdw_refined 0.303 r_symmetry_hbond_refined 0.235 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.211 r_chiral_restr 0.089 r_metal_ion_refined 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other 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 14508 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling DM phasing