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Structure of AAC(6')-Ib in complex with Ribostamycin and Coenzyme A.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V0C PDB ENTRY 1V0C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.75 PROTEIN (10MG/ML, 20 MM TRIS PH 7.5, 20 MM NACL, 3 MM ACCOA) PRECIPITANT (20% PEG3350, 200 MM CALCIUM ACETATE, 100 MM NACACODYLATE PH 6.75) VAPOR DIFFUSION UNDER OIL
Crystal Properties Matthews coefficient Solvent content 2.46 55.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.475 α = 90 b = 57.475 β = 90 c = 148.305 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 93 IMAGE PLATE RIGAKU-MSC RAXIS-IV 2006-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 1.7 24.29 97 0.04 33.2 7.4 27341
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 1.7 1.79 84.7 0.21 6.9 6
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 1V0C 1.7 149.07 25956 1382 96.4 0.184 0.182 0.1799 0.211 0.2091 RANDOM 17.58
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] 0.12 0.12 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.549 r_dihedral_angle_4_deg 15.64 r_dihedral_angle_3_deg 12.183 r_dihedral_angle_1_deg 5.248 r_scangle_it 3.461 r_scbond_it 2.15 r_mcangle_it 1.482 r_angle_refined_deg 1.335 r_mcbond_it 0.928 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.549 r_dihedral_angle_4_deg 15.64 r_dihedral_angle_3_deg 12.183 r_dihedral_angle_1_deg 5.248 r_scangle_it 3.461 r_scbond_it 2.15 r_mcangle_it 1.482 r_angle_refined_deg 1.335 r_mcbond_it 0.928 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.228 r_symmetry_vdw_refined 0.202 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined 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_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 1404 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling