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Crystal structure of putative diphthine synthase from Entamoeba histolytica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EGL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 289 PACT screen condition A6, SPG buffer 0.1 M each succinic acid, phosphate and glycine, 25% PEG 1500, 34.4 mg/mL, crystal tracking ID 203532a6, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.41 49.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.894 α = 90 b = 84.894 β = 90 c = 89.402 γ = 90
Symmetry Space Group P 43 2 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 CCD ADSC QUANTUM 315 2009-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 2.49 42.45 97.9 0.114 14 5.9 11655
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) 2.49 2.59 99.1 0.689 2.5 5.9
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 2EGL 2.49 42.45 11067 587 97.81 0.22649 0.22405 0.2183 0.27306 0.2321 RANDOM 43.908
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] -0.42 -0.42 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.99 r_dihedral_angle_4_deg 17.635 r_dihedral_angle_3_deg 16.022 r_dihedral_angle_1_deg 5.765 r_scangle_it 2.627 r_scbond_it 1.561 r_angle_refined_deg 1.204 r_mcangle_it 1.14 r_mcbond_it 0.593 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.99 r_dihedral_angle_4_deg 17.635 r_dihedral_angle_3_deg 16.022 r_dihedral_angle_1_deg 5.765 r_scangle_it 2.627 r_scbond_it 1.561 r_angle_refined_deg 1.204 r_mcangle_it 1.14 r_mcbond_it 0.593 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 1989 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling