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Crystal structure of Entamoeba histolytica Malic Enzyme
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 1.5M Ammonium Sulfate, sodium acetate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.56 51.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.731 α = 90 b = 117.731 β = 90 c = 157.615 γ = 90
Symmetry Space Group P 43 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.25 94.32 53238 53238 3 3
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 2.25 47.16 0.068 32.3 26.2 53238
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SIRAS THROUGHOUT 2.25 47.16 50457 2704 99.95 0.18253 0.1792 0.1765 0.24463 0.2404 RANDOM 29.373
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] 0.11 0.11 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.686 r_dihedral_angle_4_deg 20.752 r_dihedral_angle_3_deg 16.371 r_dihedral_angle_1_deg 6.281 r_scangle_it 4.306 r_scbond_it 2.794 r_angle_refined_deg 1.834 r_mcangle_it 1.539 r_mcbond_it 0.867 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.686 r_dihedral_angle_4_deg 20.752 r_dihedral_angle_3_deg 16.371 r_dihedral_angle_1_deg 6.281 r_scangle_it 4.306 r_scbond_it 2.794 r_angle_refined_deg 1.834 r_mcangle_it 1.539 r_mcbond_it 0.867 r_chiral_restr 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7466 Nucleic Acid Atoms Solvent Atoms 582 Heterogen Atoms 137
Software Software Software Name Purpose d*TREK data scaling SHARP phasing SOLOMON phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection d*TREK data reduction