☰ Navigation Tabs
60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II) and N-oxalylglycine (NOG)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DIQ PDB ENTRY 4DIQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 VAPOR DIFFUSION, SITTING DROP 0.1M BIS-TRIS PROPANE PH 5.6-6.5, 0.5-0.7M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.97 58.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.41 α = 90 b = 80.71 β = 94.54 c = 151.54 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 DECTRIS PILATUS 2M MIRRORS 2012-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 2.15 81.1 98.9 0.08 10.2 4.5 131084 2 37.3
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 2.15 2.21 97.9 0.66 2.2 4.4
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 4DIQ 2.15 81.1 131084 6594 98.9 0.186 0.186 0.1989 0.197 0.2068 RANDOM 43.1
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] -1.19 1.9 6.52 -5.33
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_angle_deg 1.3 c_improper_angle_d 1.04 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_angle_deg 1.3 c_improper_angle_d 1.04 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14530 Nucleic Acid Atoms Solvent Atoms 829 Heterogen Atoms 60
Software Software Software Name Purpose CNS refinement MOSFLM data reduction SCALA data scaling PHASER phasing