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An ancestral arginine-binding protein bound to arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.2 M Li2SO4, 0.1 M HEPES pH 7.5, 27.5% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.53 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.46 α = 90 b = 60.41 β = 90 c = 103.99 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 210r 2013-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
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 28.56 99.6 0.093 12 6.9 40887
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 1.52 1.55 94.4 0.612 2.4 4.7
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 1WDN 1.52 28.56 38763 2052 99.48 0.17154 0.16998 0.1818 0.2005 0.2103 RANDOM 14.732
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.19 r_dihedral_angle_3_deg 13.924 r_dihedral_angle_4_deg 10.157 r_long_range_B_refined 6.702 r_long_range_B_other 6.425 r_dihedral_angle_1_deg 6.341 r_scangle_other 4.313 r_scbond_it 2.84 r_scbond_other 2.84 r_mcangle_it 2.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.19 r_dihedral_angle_3_deg 13.924 r_dihedral_angle_4_deg 10.157 r_long_range_B_refined 6.702 r_long_range_B_other 6.425 r_dihedral_angle_1_deg 6.341 r_scangle_other 4.313 r_scbond_it 2.84 r_scbond_other 2.84 r_mcangle_it 2.549 r_mcangle_other 2.548 r_angle_refined_deg 2.318 r_mcbond_it 1.691 r_mcbond_other 1.691 r_angle_other_deg 0.938 r_chiral_restr 0.133 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 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 1728 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing