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Biphenyl dioxygenase (BphA1A2) derived from Rhodococcus sp. strain RHA1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 PEG 4000, ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.62 52.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.741 α = 90 b = 137.741 β = 90 c = 237.744 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 4 2002-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL40B2 0.9796 SPring-8 BL40B2
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 1.9 50 85.8 0.075 0.075 8.7 6.4 153515 153515 16.7
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) 1 1.9 2 49 0.292 0.292 2.5 4.4 12618
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.2 38.07 110357 109044 5714 98.81 0.16893 0.16893 0.16727 0.1792 0.20067 0.2088 RANDOM 16.018
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.774 r_scangle_it 2.627 r_scbond_it 1.562 r_angle_refined_deg 1.259 r_mcangle_it 1.061 r_angle_other_deg 0.81 r_mcbond_it 0.559 r_symmetry_vdw_other 0.286 r_nbd_other 0.243 r_nbd_refined 0.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.774 r_scangle_it 2.627 r_scbond_it 1.562 r_angle_refined_deg 1.259 r_mcangle_it 1.061 r_angle_other_deg 0.81 r_mcbond_it 0.559 r_symmetry_vdw_other 0.286 r_nbd_other 0.243 r_nbd_refined 0.186 r_xyhbond_nbd_refined 0.133 r_symmetry_hbond_refined 0.122 r_metal_ion_refined 0.09 r_nbtor_other 0.083 r_symmetry_vdw_refined 0.082 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14579 Nucleic Acid Atoms Solvent Atoms 750 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing