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Conformational alternate of sisomicin in complex with APH(2")-IVa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N57
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 291.15 12% PEG3350, 50-90 mM Ammonium citrate
Crystal Properties Matthews coefficient Solvent content 2.72 54.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.22 α = 90 b = 65.04 β = 91.18 c = 78.78 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2015-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972957 ESRF ID23-1
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 2.35 37.1 94.7 0.034 8.9 1.9 29965 28377
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 2.35 2.43 96.6 0.23 2.5 1.9
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 4N57 2.35 37.1 28377 1392 94.7 0.2296 0.227 0.2299 0.2784 0.2728 RANDOM 63.306
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] 8.43 -1.09 -6.4 -1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.211 r_dihedral_angle_4_deg 20.228 r_dihedral_angle_3_deg 18.778 r_dihedral_angle_1_deg 5.86 r_mcangle_it 4.13 r_mcbond_it 2.726 r_mcbond_other 2.726 r_angle_refined_deg 1.538 r_angle_other_deg 1.225 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.211 r_dihedral_angle_4_deg 20.228 r_dihedral_angle_3_deg 18.778 r_dihedral_angle_1_deg 5.86 r_mcangle_it 4.13 r_mcbond_it 2.726 r_mcbond_other 2.726 r_angle_refined_deg 1.538 r_angle_other_deg 1.225 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4876 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction Coot model building DNA data collection