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Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 291 0.09M MES, 24% PEG 3350, 0.18mM Ca(OAc)2, 0.01mM tri-Sodium Citrate dihydrate pH 5.6, 2% iso-Propanol, 2% PEG 4000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.48 50.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.2 α = 90 b = 89.4 β = 90 c = 150.8 γ = 90
Symmetry Space Group P 21 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 315 mirrors 2006-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9791 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.55 50 99 0.076 0.076 21.9 7.1 39165 39165 -3 64.2
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) 2.55 2.64 93.6 0.26 0.26 3.85 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.55 20 39098 39165 2753 99 0.24 0.24 0.2399 0.27 0.2708 RANDOM 58.87
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] 0.662 -21.578 20.916
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.64 c_scangle_it 2.537 c_mcangle_it 1.986 c_improper_angle_d 1.75 c_angle_deg 1.72 c_scbond_it 1.669 c_mcbond_it 1.17 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.64 c_scangle_it 2.537 c_mcangle_it 1.986 c_improper_angle_d 1.75 c_angle_deg 1.72 c_scbond_it 1.669 c_mcbond_it 1.17 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4800 Nucleic Acid Atoms 3046 Solvent Atoms 162 Heterogen Atoms 7
Software Software Software Name Purpose SHELXD phasing SOLVE phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling