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Crystal Structure of catalytic fragment of E. coli AlaRS in complex with GlySA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 277 31% PEG 400, 0.1 M HEPES, pH 7.9, vapor diffusion, sitting drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.13 70.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.639 α = 90 b = 114.639 β = 90 c = 125.398 γ = 90
Symmetry Space Group P 41 21 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 CCD ADSC QUANTUM 315r 2008-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.97950 SSRL BL9-1
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 1.93 50 92 0.042 35.739 6.1 58254
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 1.93 2 94.3 0.123 6
Refinement Statistics Diffraction ID Structure Solution Method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1.93 50 58211 2988 92 0.161 0.159 0.1595 0.188 0.1864 21.03
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] -0.32 -0.32 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.172 r_dihedral_angle_4_deg 13.903 r_dihedral_angle_3_deg 10.445 r_scangle_it 7.425 r_scbond_it 5.406 r_dihedral_angle_1_deg 4.793 r_mcangle_it 4.596 r_mcbond_it 4.35 r_angle_refined_deg 1.063 r_chiral_restr 0.384
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.172 r_dihedral_angle_4_deg 13.903 r_dihedral_angle_3_deg 10.445 r_scangle_it 7.425 r_scbond_it 5.406 r_dihedral_angle_1_deg 4.793 r_mcangle_it 4.596 r_mcbond_it 4.35 r_angle_refined_deg 1.063 r_chiral_restr 0.384 r_nbtor_refined 0.319 r_symmetry_hbond_refined 0.203 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.182 r_symmetry_vdw_refined 0.171 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3516 Nucleic Acid Atoms Solvent Atoms 598 Heterogen Atoms 70
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection