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NAPHTHALENE 1,2-DIOXYGENASE, FULLY REDUCED FORM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NDO PDB ENTRY 1NDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 AMMONIUM SULPHATE 2M, MES 0.1M, DIOXANE 2-3%, pH 6.00
Crystal Properties Matthews coefficient Solvent content 2.56 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.526 α = 90 b = 139.526 β = 90 c = 208.103 γ = 120
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 CCD TOROIDAL MIRROR 1999-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.9 50 94.4 0.061 10.5 6.3 57814
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 1.9 1.97 96.6 0.233 2.1 4.5
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-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 1NDO 1.9 30 54884 2921 94.4 0.181 0.1793 0.208 0.2022 RANDOM 26.01
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] 0.49 0.25 0.49 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.034 r_dihedral_angle_1_deg 5.813 r_scangle_it 3.768 r_scbond_it 2.236 r_mcangle_it 1.489 r_angle_refined_deg 1.433 r_angle_other_deg 1.043 r_mcbond_it 0.76 r_nbd_refined 0.212 r_nbd_other 0.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.034 r_dihedral_angle_1_deg 5.813 r_scangle_it 3.768 r_scbond_it 2.236 r_mcangle_it 1.489 r_angle_refined_deg 1.433 r_angle_other_deg 1.043 r_mcbond_it 0.76 r_nbd_refined 0.212 r_nbd_other 0.201 r_symmetry_vdw_other 0.201 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.101 r_symmetry_hbond_refined 0.077 r_bond_refined_d 0.012 r_xyhbond_nbd_other 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_metal_ion_refined r_metal_ion_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 5088 Nucleic Acid Atoms Solvent Atoms 378 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing