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Crystal structure of E. coli seryl-tRNA synthetase complexed to seryl sulfamoyl adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M sodium phosphate monobasic monohydrate, pH 4.7
20 % w/v PEG 3350
25 % ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.8 56.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.07 α = 75.44 b = 63.52 β = 70.25 c = 75.89 γ = 89.2
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 PILATUS3 6M 2015-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.5 61.29 95.5 0.997 9.3 2.4 163583 20.15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53
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 2DQ3 1.5 59.18 163577 7960 95.5 0.163 0.162 0.158 0.18 0.1736 RANDOM 25.95
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] -2.7811 1.5088 3.2725 2.1749 -1.1801 0.6062
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.4 t_omega_torsion 4.18 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.4 t_omega_torsion 4.18 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6649 Nucleic Acid Atoms Solvent Atoms 895 Heterogen Atoms 146
Software Software Software Name Purpose BUSTER refinement iMOSFLM data reduction Aimless data scaling PHASER phasing