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60S ribosomal protein L8 histidine hydroxylase (NO66 L299C/C300S) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-2)
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 7.4, 0.4M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.92 57.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.165 α = 90 b = 83.721 β = 100.35 c = 97.034 γ = 90
Symmetry Space Group C 1 2 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 6M MIRRORS 2013-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 2.23 44.19 98.2 0.11 7.3 3.2 58651 2 35.15
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 2.23 2.35 97.8 0.76 1.8 3.2
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 2.23 44.19 58651 2956 98.2 0.238 0.238 0.2412 0.248 0.2472 RANDOM 37.4
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] -7.34 -1.26 6.74 0.6
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_angle_deg 1.3 c_improper_angle_d 0.99 c_bond_d 0.008 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 23.4 c_angle_deg 1.3 c_improper_angle_d 0.99 c_bond_d 0.008 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 7417 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 36
Software Software Software Name Purpose CNS refinement XDS data reduction SCALA data scaling PHASER phasing