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Structure of the arginine-bound form of truncated (residues 20-233) ArgBP from T. maritima
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PSH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 The crystals were obtained using a protein concentration of 16 mg/mL and in 0.1 M Cadmium chloride hydrate, 0.1 M Sodium acetate trihydrate (pH 4.6), 30% (v/v) Polyethylene glycol 400. Crystal quality was enhanced in presence of 2.0 M Sodium Thiocyanate or 1.0 M Sodium Bromide.
Crystal Properties Matthews coefficient Solvent content 34.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.7 α = 90 b = 52.139 β = 90 c = 221.343 γ = 90
Symmetry Space Group P 21 2 21
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 MARMOSAIC 225 mm CCD 2011-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.5418 ESRF BM14
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 2.6 20 85.6 0.084 20.7 4.2 9570
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 2.6 2.64
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 4PSH 2.69 15 7711 378 76.76 0.17723 0.1748 0.22599 0.2404 RANDOM 19.371
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] 0.04 0.28 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.552 r_dihedral_angle_4_deg 19.964 r_dihedral_angle_3_deg 19.226 r_dihedral_angle_1_deg 6.288 r_scangle_it 2.826 r_scbond_it 1.666 r_angle_refined_deg 1.503 r_mcangle_it 0.963 r_mcbond_it 0.501 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.552 r_dihedral_angle_4_deg 19.964 r_dihedral_angle_3_deg 19.226 r_dihedral_angle_1_deg 6.288 r_scangle_it 2.826 r_scbond_it 1.666 r_angle_refined_deg 1.503 r_mcangle_it 0.963 r_mcbond_it 0.501 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3311 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing