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Crystal structure of domain 2 from TmArgBP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PRS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Crystals of the D2 domain were obtained using a protein concentration of 14 mg/ml in a solution containing 0.1M Bis-Tris (pH 6.5) and 28% (w/v) polyethylene glycol 2,000.
Crystal Properties Matthews coefficient Solvent content 1.75 29.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.619 α = 90 b = 49.73 β = 100.19 c = 27.782 γ = 90
Symmetry Space Group P 1 21 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 CCD RIGAKU SATURN 944 2016-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 1.73 15 95.1 0.04 30.2 1.3 6898
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 1.73 1.77
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 4PRS 1.73 14.18 6554 322 95.62 0.13137 0.12949 0.1442 0.16847 0.1762 RANDOM 16.651
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] 0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.608 r_dihedral_angle_3_deg 12.105 r_dihedral_angle_4_deg 9.298 r_dihedral_angle_1_deg 5.917 r_long_range_B_refined 5.753 r_long_range_B_other 4.823 r_scangle_other 2.625 r_scbond_it 1.727 r_scbond_other 1.72 r_angle_refined_deg 1.674
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.608 r_dihedral_angle_3_deg 12.105 r_dihedral_angle_4_deg 9.298 r_dihedral_angle_1_deg 5.917 r_long_range_B_refined 5.753 r_long_range_B_other 4.823 r_scangle_other 2.625 r_scbond_it 1.727 r_scbond_other 1.72 r_angle_refined_deg 1.674 r_mcangle_other 1.469 r_mcangle_it 1.466 r_mcbond_it 1.036 r_mcbond_other 1.026 r_angle_other_deg 0.798 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 703 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing