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Crystal structure of the MLLE domain of poly(A)-binding protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I2T pdb entry 1I2T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 295 1.3M ammonium sulfate, 0.5M lithium sulfate, 5% glycerol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.3 62.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.977 α = 90 b = 146.977 β = 90 c = 83.055 γ = 90
Symmetry Space Group P 43 21 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 210 mirrors 2009-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 0.9950 CHESS F2
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 2.5 103.7 96.7 0.076 23.1 6.3 30434 29430 1 1
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 2.5 2.57 73.5 0.4 2.8 5.4 1602
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1I2T 2.5 50 1 30434 29430 1558 96.71 0.21841 0.21566 0.2138 0.27224 0.2696 RANDOM 33.041
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] 1.31 1.31 -2.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.352 r_dihedral_angle_3_deg 22.719 r_dihedral_angle_4_deg 20.015 r_dihedral_angle_1_deg 5.385 r_scangle_it 3.804 r_scbond_it 2.239 r_angle_refined_deg 1.676 r_mcangle_it 1.251 r_mcbond_it 0.77 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.352 r_dihedral_angle_3_deg 22.719 r_dihedral_angle_4_deg 20.015 r_dihedral_angle_1_deg 5.385 r_scangle_it 3.804 r_scbond_it 2.239 r_angle_refined_deg 1.676 r_mcangle_it 1.251 r_mcbond_it 0.77 r_nbtor_refined 0.315 r_nbd_refined 0.253 r_symmetry_vdw_refined 0.243 r_xyhbond_nbd_refined 0.173 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.117 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4384 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 5
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling