☰ Navigation Tabs
Crystal structure of the PFV N224H mutant intasome bound to manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OY9 PDB entry 3OY9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 1.35 M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50 mM Mes-NaOH, 1mM EDTA, pH 6.5, vapor diffusion, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.81 67.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.05 α = 90 b = 158.05 β = 90 c = 122.16 γ = 90
Symmetry Space Group P 41 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 315 2010-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97630 Diamond I04
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 2.02 39.894 98.9 0.106 8.7 4.8 99967 -3 -3
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) 2.02 2.13 98.8 0.761 0.761 1.6 4.9 14403
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 (All) 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 3OY9 2.02 39.89 99745 5025 98.52 0.2 0.1987 0.1972 0.1977 0.2276 0.2274 RANDOM 37.6561
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] 1.09 1.09 -2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.347 r_dihedral_angle_4_deg 14.443 r_dihedral_angle_3_deg 14.05 r_dihedral_angle_1_deg 5.81 r_scangle_it 2.877 r_scbond_it 1.773 r_angle_refined_deg 1.353 r_mcangle_it 1.259 r_mcbond_it 0.662 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.347 r_dihedral_angle_4_deg 14.443 r_dihedral_angle_3_deg 14.05 r_dihedral_angle_1_deg 5.81 r_scangle_it 2.877 r_scbond_it 1.773 r_angle_refined_deg 1.353 r_mcangle_it 1.259 r_mcbond_it 0.662 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4388 Nucleic Acid Atoms 732 Solvent Atoms 596 Heterogen Atoms 58
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection