☰ Navigation Tabs
Crystal Structure of an Acyl-CoA Binding Protein (LmjF.17.0620) of Leishmania major
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 291 0.1M Sodium Citrate tribasic dihydrate,
10%(v/v) 2-Propanol, 20%(w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 2.02 39.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.989 α = 103.81 b = 29.076 β = 110.42 c = 33.778 γ = 95
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ Varimax HF 2014-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
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 1.46 30.31 88.3 0.022 17.62 3.5 14140 -3 14.5
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 1.46 1.51 73.6 0.075 15.98 3.3
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 3FP5 1.46 30.31 13433 707 89.26 0.16076 0.15983 0.1604 0.17699 0.178 RANDOM 17.28
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] 0.31 -0.23 0.5 -0.6 -0.29 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.273 r_dihedral_angle_4_deg 15.188 r_dihedral_angle_3_deg 12.867 r_long_range_B_refined 5.587 r_long_range_B_other 5.22 r_dihedral_angle_1_deg 5.185 r_scangle_other 3.808 r_scbond_it 2.938 r_scbond_other 2.935 r_mcangle_other 2.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.273 r_dihedral_angle_4_deg 15.188 r_dihedral_angle_3_deg 12.867 r_long_range_B_refined 5.587 r_long_range_B_other 5.22 r_dihedral_angle_1_deg 5.185 r_scangle_other 3.808 r_scbond_it 2.938 r_scbond_other 2.935 r_mcangle_other 2.784 r_mcangle_it 2.777 r_angle_refined_deg 2.175 r_mcbond_it 2.134 r_mcbond_other 1.972 r_angle_other_deg 1.135 r_chiral_restr 0.136 r_bond_refined_d 0.024 r_gen_planes_refined 0.013 r_bond_other_d 0.004 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 751 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing