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crystal structure analysis of eukaryotic translation initiation factor 5B and 1A complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WBI PDB ENTRY 3WBI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 293 100mM Tris-HCl pH 8.2, 12.5%(w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.72 54.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.939 α = 90 b = 120.942 β = 90 c = 132.75 γ = 90
Symmetry Space Group P 21 21 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 RAYONIX MX225HE 2010-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.980 SPring-8 BL41XU
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 3.3 50 98.5 0.071 16.2 9.4 24875 -1.15
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 3.3 3.42 92.9 0.492 5.8 2318
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 PDB ENTRY 3WBI 3.3 40 24828 1769 98.23 0.2613 0.257 0.2539 0.3173 0.3176 RANDOM 159.3338
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] -12.35 1.66 10.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.689 r_dihedral_angle_4_deg 19.763 r_dihedral_angle_3_deg 18.218 r_mcangle_it 16.555 r_scbond_it 11.418 r_mcbond_it 10.383 r_dihedral_angle_1_deg 6.026 r_angle_refined_deg 1.306 r_chiral_restr 0.081 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.689 r_dihedral_angle_4_deg 19.763 r_dihedral_angle_3_deg 18.218 r_mcangle_it 16.555 r_scbond_it 11.418 r_mcbond_it 10.383 r_dihedral_angle_1_deg 6.026 r_angle_refined_deg 1.306 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9309 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing