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The 1.4 Ang crystal structure of the ArsD arsenic metallochaperone provides insights into its interactions with the ArsA ATPase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KGK PDB entry 3KGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 25% PEG 6000, 0.1M Calcium acetate, 0.1M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 47.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.676 α = 90 b = 74.223 β = 97.77 c = 40.83 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 IMAGE PLATE RIGAKU RAXIS HTC MIRROR 2007-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-D 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.05 40.46 97.8 0.091 3.12 13712
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 2.05 2.12 98.6 0.348 3.05 13712
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 PDB entry 3KGK 2.05 40.46 13712 686 97.72 0.27351 0.27098 0.2586 0.32419 0.325 RANDOM 37.96
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] -0.88 1.52 -2.05 3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.865 r_dihedral_angle_3_deg 19.267 r_dihedral_angle_4_deg 16.935 r_dihedral_angle_1_deg 7.374 r_scangle_it 4.7 r_scbond_it 3.148 r_angle_refined_deg 1.992 r_mcangle_it 1.966 r_mcbond_it 1.129 r_chiral_restr 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.865 r_dihedral_angle_3_deg 19.267 r_dihedral_angle_4_deg 16.935 r_dihedral_angle_1_deg 7.374 r_scangle_it 4.7 r_scbond_it 3.148 r_angle_refined_deg 1.992 r_mcangle_it 1.966 r_mcbond_it 1.129 r_chiral_restr 0.141 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1534 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 6
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling