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Crystal structure of aminoglycoside phosphotransferase APH(2'')-Ib, apo form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.2 M MG CHLORIDE, 0.1 M HEPES PH 7.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.22 44.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.72 α = 90 b = 62.219 β = 90 c = 89.726 γ = 90
Symmetry Space Group P 2 21 21
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 315r mirrors 2009-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97940 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 20 97.9 0.086 23.28 4.5 24877 25410 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 86.5 0.391 2.61 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.95 19.93 22090 1179 91.62 0.19643 0.19382 0.2012 0.24536 0.2543 RANDOM 29.454
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] 2.5 -0.89 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.304 r_dihedral_angle_4_deg 10.792 r_dihedral_angle_3_deg 9.229 r_scangle_it 4.807 r_scbond_it 3.068 r_dihedral_angle_1_deg 2.687 r_mcangle_it 1.701 r_angle_refined_deg 1.251 r_mcbond_it 0.972 r_angle_other_deg 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.304 r_dihedral_angle_4_deg 10.792 r_dihedral_angle_3_deg 9.229 r_scangle_it 4.807 r_scbond_it 3.068 r_dihedral_angle_1_deg 2.687 r_mcangle_it 1.701 r_angle_refined_deg 1.251 r_mcbond_it 0.972 r_angle_other_deg 0.8 r_mcbond_other 0.308 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2489 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 37
Software Software Software Name Purpose HKL-2000 data collection SHELXS phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling