☰ Navigation Tabs
Crystal structure of aminoglycoside-3'-phosphotransferase of type VIII
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R78
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 278 0.1M Sodium citrate; 18% PEG20K, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.36 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.34 α = 90 b = 103.34 β = 94.36 c = 53.68 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 CCD MAR CCD 165 mm 2012-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.985 KURCHATOV SNC K4.4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.15 28.97 99.9 30435 30335 35.081
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.206 99.9 2.63 36911
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 3R78 2.15 28.97 30435 30335 1536 99.92 0.198 0.1943 0.1978 0.2684 0.2667 RANDOM 38.7243
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] 0.18 0.15 -0.14 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.399 r_dihedral_angle_4_deg 21.692 r_dihedral_angle_3_deg 20.88 r_dihedral_angle_1_deg 8.555 r_angle_refined_deg 2.348 r_angle_other_deg 1.422 r_chiral_restr 0.143 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.399 r_dihedral_angle_4_deg 21.692 r_dihedral_angle_3_deg 20.88 r_dihedral_angle_1_deg 8.555 r_angle_refined_deg 2.348 r_angle_other_deg 1.422 r_chiral_restr 0.143 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4110 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XDS data reduction XSCALE data scaling BALBES phasing