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Crystal structure of a histidine triad family protein from Entamoeba histolytica, bound to GMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OMF 3OMF, with ligand and water molecules removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 290 Internal tracking number 217759B6. 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 + ~30 mM GMP, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.16 43.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.66 α = 90 b = 60.86 β = 90 c = 67.93 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 2010-09-17 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 1.55 27.77 90.3 0.05 25.18 6.6 16495 14890 -3 18.008
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 1.55 1.59 82.4 0.391 3.8 5.2 1185
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 3OMF, with ligand and water molecules removed 1.55 27.77 16495 14847 712 90.01 0.159 0.159 0.157 0.1706 0.208 0.218 RANDOM 11.794
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] 0.03 -0.61 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.591 r_dihedral_angle_4_deg 19.829 r_dihedral_angle_3_deg 11.262 r_dihedral_angle_1_deg 6.264 r_scangle_it 3.162 r_scbond_it 2.049 r_angle_refined_deg 1.628 r_mcangle_it 1.29 r_angle_other_deg 0.898 r_mcbond_it 0.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.591 r_dihedral_angle_4_deg 19.829 r_dihedral_angle_3_deg 11.262 r_dihedral_angle_1_deg 6.264 r_scangle_it 3.162 r_scbond_it 2.049 r_angle_refined_deg 1.628 r_mcangle_it 1.29 r_angle_other_deg 0.898 r_mcbond_it 0.756 r_mcbond_other 0.216 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 897 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 28
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction