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Computationally Designed Self-assembling tetrahedron protein, T310
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DCL pdb entry 4DCL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 7.5% polyethylene glycol 2000 monomethyl ether, 0.1 M sodium citrate, pH 6.0, 35% glycerol as cryoprotectant, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.66 53.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.76 α = 90 b = 90.84 β = 125.3 c = 107.7 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2012-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9793 APS 24-ID-C
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 2.21 100 96.8 0.106 8.1 6 69236 69236 -3 57.1
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 2.25 2.33 93.4 0.553 2.4 6615
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 4DCL 2.21 22.28 67098 67098 3386 92.64 0.2092 0.2076 0.2385 0.2515 RANDOM 65.7481
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] 2.1133 -10.0641 -0.6236 -1.4896
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.43 t_omega_torsion 3.13 t_angle_deg 1.11 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.43 t_omega_torsion 3.13 t_angle_deg 1.11 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8728 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 48
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing BUSTER-TNT refinement PDB_EXTRACT data extraction BUSTER refinement