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Crystal structure of the ligand-free form of domain 1 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 5.5 293 The best crystals of D1 domain were obtained using a protein concentration of 6 mg/ml in a solution containing 0.2 M NaCl, 0.1M Bis-Tris (pH 5.5), 25% (w/v) polyethylene glycol (PEG) 3,350.
Crystal Properties Matthews coefficient Solvent content 2.57 52.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.445 α = 116.01 b = 46.036 β = 109.85 c = 52.496 γ = 90.01
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 2015-02-26 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 1.75 15 88.8 0.044 37.2 2.7 24812
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 1.75 1.78
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4PRS 1.75 14.4 23533 1240 88.59 0.16502 0.16374 0.18833 0.1952 RANDOM 18.293
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] 0.01 0.01 -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.941 r_dihedral_angle_4_deg 17.022 r_dihedral_angle_3_deg 12.102 r_long_range_B_refined 7.449 r_long_range_B_other 7.306 r_dihedral_angle_1_deg 5.681 r_scangle_other 4.316 r_scbond_it 2.853 r_scbond_other 2.852 r_mcangle_it 2.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.941 r_dihedral_angle_4_deg 17.022 r_dihedral_angle_3_deg 12.102 r_long_range_B_refined 7.449 r_long_range_B_other 7.306 r_dihedral_angle_1_deg 5.681 r_scangle_other 4.316 r_scbond_it 2.853 r_scbond_other 2.852 r_mcangle_it 2.808 r_mcangle_other 2.807 r_angle_refined_deg 1.95 r_mcbond_it 1.83 r_mcbond_other 1.83 r_angle_other_deg 0.891 r_chiral_restr 0.116 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 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 1950 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing