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Crystal structure of Isocitrate lyase-1 from Candida albicans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EBC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 22%(w/v)PEG 3350, 0.2M magnesium formate
Crystal Properties Matthews coefficient Solvent content 2.31 46.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.971 α = 90 b = 139.91 β = 92.55 c = 200.301 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 16M 2020-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.69 200.1 99.5 0.0693 0.0732 0.0387 0.998 13.5 3.5 122958
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.69 2.79 0.595 0.7 0.366 0.849
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 7EBC 2.69 47.11 116812 6148 99.52 0.21634 0.21468 0.217 0.24797 0.2481 RANDOM 74.4
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 0.02 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.588 r_dihedral_angle_4_deg 21.829 r_dihedral_angle_3_deg 19.754 r_dihedral_angle_1_deg 8.705 r_long_range_B_refined 7.24 r_long_range_B_other 7.24 r_scangle_other 5.648 r_mcangle_it 5.451 r_mcangle_other 5.451 r_scbond_it 3.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.588 r_dihedral_angle_4_deg 21.829 r_dihedral_angle_3_deg 19.754 r_dihedral_angle_1_deg 8.705 r_long_range_B_refined 7.24 r_long_range_B_other 7.24 r_scangle_other 5.648 r_mcangle_it 5.451 r_mcangle_other 5.451 r_scbond_it 3.898 r_scbond_other 3.898 r_mcbond_it 3.744 r_mcbond_other 3.744 r_angle_other_deg 0.473 r_angle_refined_deg 0.398 r_chiral_restr 0.036 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33985 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing