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Crystal structure of URE3-binding protein from Entamoeba histolytica, (D127A,N129A) mutant, native form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SIA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 290 Internal tracking number 215760A3. Focus screen based on CryoFull G6. 1 uL 40% PEG600, 0.1 M citrate pH 4.56 + 1 uL EnhiA.01648.a.D18 PD00123 (VCID3088) at 9.5 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.09 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.25 α = 90 b = 68.29 β = 90 c = 130.89 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+ 2010-06-16 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 1.9 38.29 99.4 0.055 17.42 5.05 16665 -3 30.04
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 1.9 1.95 96.3 0.431 2.4 2.746
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 3SIA 1.9 38.29 16655 651 99.86 0.174 0.172 0.18 0.221 0.2223 RANDOM 23.09
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] 0.9 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.761 r_dihedral_angle_4_deg 18.892 r_dihedral_angle_3_deg 13.457 r_dihedral_angle_1_deg 5.409 r_scangle_it 3.803 r_scbond_it 2.417 r_angle_refined_deg 1.452 r_mcangle_it 1.338 r_angle_other_deg 0.954 r_mcbond_it 0.719
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.761 r_dihedral_angle_4_deg 18.892 r_dihedral_angle_3_deg 13.457 r_dihedral_angle_1_deg 5.409 r_scangle_it 3.803 r_scbond_it 2.417 r_angle_refined_deg 1.452 r_mcangle_it 1.338 r_angle_other_deg 0.954 r_mcbond_it 0.719 r_mcbond_other 0.189 r_chiral_restr 0.085 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1722 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 2
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing