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Crystal structure of the C558(464)A/C559(465)A double mutant of Tn501 MerA in complex with NADPH and Hg2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GRS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.4 295 2.0M AMMONIA Sulfate, 0.1M Tris, pH 9.4, vapor diffusion hanging drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.63 53.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.922 α = 90 b = 86.922 β = 90 c = 137.19 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 2002-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.90 APS 14-BM-C
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 1.86 60 99.9 0.064 0.064 32.8 8.9 45046
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 1.86 1.89 100 0.561 0.561 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 (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 3GRS 1.86 28.36 45046 44048 923 99.9 0.16815 0.16742 0.1799 0.20342 0.2154 RANDOM 26.449
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] 0.86 0.86 -1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.195 r_dihedral_angle_4_deg 16.624 r_dihedral_angle_3_deg 12.876 r_dihedral_angle_1_deg 5.646 r_mcangle_it 2.31 r_scbond_it 1.766 r_mcbond_it 1.42 r_mcbond_other 1.417 r_angle_refined_deg 1.415 r_angle_other_deg 0.749
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.195 r_dihedral_angle_4_deg 16.624 r_dihedral_angle_3_deg 12.876 r_dihedral_angle_1_deg 5.646 r_mcangle_it 2.31 r_scbond_it 1.766 r_mcbond_it 1.42 r_mcbond_other 1.417 r_angle_refined_deg 1.415 r_angle_other_deg 0.749 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3400 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection DENZO data reduction SCALEPACK data scaling GLRF phasing