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Crystal structure of a histidine triad family protein from Entamoeba histolytica, bound to AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OJ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 289 Internal tracking number 217183B6. JCSG screen condition B6:
40% v/v ethanol, 5% w/v PEG 1000, phosphate-citrate buffer pH 4.2, EnhiA.01296.a.A1
PS00632 at 83.2 mg/ml, 10 mM AMP, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.12 41.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.58 α = 90 b = 60.63 β = 90 c = 67.88 γ = 90
Symmetry Space Group C 2 2 21
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 RIGAKU SATURN 944+ 2010-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.541780
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 1.8 34.56 91.6 0.023 52.96 5.8 10570 9684 -3 16.256
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 1.8 1.85 80.3 0.045 21.4 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR, MR THROUGHOUT 3OJ7 1.8 34.56 10570 9660 467 91.39 0.148 0.148 0.146 0.191 0.1886 RANDOM 9.817
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] 0.25 -0.21 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.727 r_dihedral_angle_4_deg 20.708 r_dihedral_angle_3_deg 12.426 r_dihedral_angle_1_deg 6.332 r_scangle_it 3.185 r_scbond_it 1.922 r_angle_refined_deg 1.516 r_mcangle_it 1.197 r_angle_other_deg 0.901 r_mcbond_it 0.639
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.727 r_dihedral_angle_4_deg 20.708 r_dihedral_angle_3_deg 12.426 r_dihedral_angle_1_deg 6.332 r_scangle_it 3.185 r_scbond_it 1.922 r_angle_refined_deg 1.516 r_mcangle_it 1.197 r_angle_other_deg 0.901 r_mcbond_it 0.639 r_mcbond_other 0.165 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 879 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 24
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction