☰ Navigation Tabs
Crystal structure of a human tRNAGly acceptor stem microhelix (derived from the gene sequence DG9990) at 1.18 Angstroem resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V7R PDB ENTRY 2V7R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 294 10% (V/V) MPD, 40 MM SODIUM CACODYLATE, PH 6.0, 12 MM SPERMINE TETRACHLORIDE, 80 MM POTASSIUM CHLORIDE, EQUILIBRATED AGAINST 35 % (V/V) MPD AT 294 K.
Crystal Properties Matthews coefficient Solvent content 2.07 40.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.318 α = 90 b = 37.613 β = 112.6 c = 30.465 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 CCD ADSC CCD 2008-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.18 50 94 0.08 22.9 11.1 12058 2
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 1.18 1.22 87 0.21 1.8 7.5
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 2V7R 1.18 22.25 11449 601 93.75 0.2052 0.20405 0.221 0.22806 0.2062 RANDOM 11.02
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] -0.02 -0.01 0.07 -0.05
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.29 r_scbond_it 1.892 r_angle_refined_deg 1.627 r_nbtor_refined 0.273 r_nbd_refined 0.162 r_xyhbond_nbd_refined 0.119 r_symmetry_vdw_refined 0.112 r_symmetry_hbond_refined 0.067 r_chiral_restr 0.056 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.29 r_scbond_it 1.892 r_angle_refined_deg 1.627 r_nbtor_refined 0.273 r_nbd_refined 0.162 r_xyhbond_nbd_refined 0.119 r_symmetry_vdw_refined 0.112 r_symmetry_hbond_refined 0.067 r_chiral_restr 0.056 r_gen_planes_refined 0.012 r_bond_refined_d 0.008 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 292 Solvent Atoms 48 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PHASER phasing