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Crystal structure of DH domain of FYVE Domain containing protein(FP10) from Entamoeba histolytica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 1.5M Sodium Citrate tribasic dihydrate, 0.1M Sodium Citrate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.12 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.59 α = 90 b = 69.337 β = 118.275 c = 57.615 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 2021-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
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 2.48 50.741 90.4 0.99 2.6 7.1 16337
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 5.544 0.93
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.48 50.741 12690 697 90.404 0.237 0.2339 0.2355 0.2893 0.2855 39.861
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] -4.04 -1.922 6.717 -0.386
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.102 r_dihedral_angle_6_deg 15.331 r_dihedral_angle_2_deg 11.925 r_lrange_it 11.517 r_lrange_other 11.516 r_scangle_other 8.164 r_scangle_it 8.162 r_mcangle_it 6.743 r_mcangle_other 6.743 r_dihedral_angle_1_deg 6.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.102 r_dihedral_angle_6_deg 15.331 r_dihedral_angle_2_deg 11.925 r_lrange_it 11.517 r_lrange_other 11.516 r_scangle_other 8.164 r_scangle_it 8.162 r_mcangle_it 6.743 r_mcangle_other 6.743 r_dihedral_angle_1_deg 6.44 r_scbond_it 5.263 r_scbond_other 5.253 r_mcbond_it 4.465 r_mcbond_other 4.465 r_angle_refined_deg 1.423 r_angle_other_deg 0.486 r_nbd_other 0.324 r_symmetry_nbd_refined 0.289 r_nbd_refined 0.247 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.19 r_symmetry_xyhbond_nbd_refined 0.158 r_ncsr_local_group_1 0.126 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.02 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3037 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling BALBES phasing