☰ Navigation Tabs
Crystal structure of the Cryptosporidium muris cytosolic leucyl-tRNA synthetase editing domain (apo structure)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WFG PDB ENTRY 2WFG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.8 0.1 M MES (PH 6.8), 2% ETHANOL AND 10% (W/V) PEG 20000. 20% (V/V) ETHYLENE GLYCOL WAS USED AS CRYOPROTECTANT.
Crystal Properties Matthews coefficient Solvent content 3.4 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.708 α = 90 b = 107.708 β = 90 c = 311.199 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 PIXEL DECTRIS PILATUS 6M 2012-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 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 2.7 48 100 0.05 30 8.7 51501 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 2.7 2.84 99 0.93 2.7 9
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 2WFG 2.7 48 48772 2609 99.84 0.20563 0.20303 0.2051 0.25561 0.2522 RANDOM 90.569
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] 0.67 0.67 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.338 r_dihedral_angle_3_deg 17.132 r_dihedral_angle_4_deg 14.681 r_dihedral_angle_1_deg 7.562 r_mcangle_it 5.03 r_scbond_it 3.263 r_mcbond_other 3.179 r_mcbond_it 3.178 r_angle_refined_deg 1.841 r_angle_other_deg 1.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.338 r_dihedral_angle_3_deg 17.132 r_dihedral_angle_4_deg 14.681 r_dihedral_angle_1_deg 7.562 r_mcangle_it 5.03 r_scbond_it 3.263 r_mcbond_other 3.179 r_mcbond_it 3.178 r_angle_refined_deg 1.841 r_angle_other_deg 1.047 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it 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 8659 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing