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Crystal structure analysis of the translation factor RF3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H5E PDB ENTRY 2h5e
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 10% PEG 8000, 0.2M calcium acetate, 0.1M sodium cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.387 α = 104.21 b = 82.795 β = 89.78 c = 148.293 γ = 89.63
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 315 2007-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 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 1.52 50 72.8 0.053 12.2 1.8 336322 244843
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.57 14 1 4709
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 (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 2h5e 1.8 33.87 202485 189405 9597 93.54 0.179 0.1769 0.1767 0.2178 0.2164 RANDOM 32.1961
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] -0.12 0.02 -0.02 0.07 0.15 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.517 r_dihedral_angle_4_deg 20.885 r_dihedral_angle_3_deg 15.461 r_dihedral_angle_1_deg 5.927 r_scangle_it 5.277 r_scbond_it 3.342 r_mcangle_it 2.117 r_angle_refined_deg 1.926 r_mcbond_it 1.263 r_chiral_restr 0.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.517 r_dihedral_angle_4_deg 20.885 r_dihedral_angle_3_deg 15.461 r_dihedral_angle_1_deg 5.927 r_scangle_it 5.277 r_scbond_it 3.342 r_mcangle_it 2.117 r_angle_refined_deg 1.926 r_mcbond_it 1.263 r_chiral_restr 0.153 r_bond_refined_d 0.022 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15528 Nucleic Acid Atoms Solvent Atoms 967 Heterogen Atoms 112
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction PHASER phasing