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Structural Analysis of a probable eukaryotic D-amino acid tRNA deacylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SeMAD model, which crystallized in a different space group (p21)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 PEG 200, MES, PEG3000, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 45.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.479 α = 90 b = 67.465 β = 90 c = 174.41 γ = 90
Symmetry Space Group P 2 2 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 2003-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.91840 ALS 8.2.2
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 1.93 47.673 79.4 0.058 0.058 10.2 3.1 48352 48177 -3 21.114
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) 1 1.93 2.02 28.6 0.238 0.238 2 2 2478
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 (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 SeMAD model, which crystallized in a different space group (p21) 1.93 46.13 45547 45547 2487 79.09 0.20053 0.20053 0.19867 0.2084 0.2343 0.2418 RANDOM 21.081
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] 0.04 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.759 r_scangle_it 6.166 r_scbond_it 3.809 r_mcangle_it 2.909 r_mcbond_it 1.749 r_angle_refined_deg 1.279 r_angle_other_deg 0.802 r_symmetry_vdw_other 0.308 r_nbd_other 0.251 r_nbd_refined 0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.759 r_scangle_it 6.166 r_scbond_it 3.809 r_mcangle_it 2.909 r_mcbond_it 1.749 r_angle_refined_deg 1.279 r_angle_other_deg 0.802 r_symmetry_vdw_other 0.308 r_nbd_other 0.251 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.127 r_nbtor_other 0.081 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5790 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing