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Crystal structure of full-length DUF199/WhiA from Thermatoga maritima
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 0.1 M Tris, pH 8.0, 0.2 M NaCl, 10% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.24 45.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.648 α = 90 b = 61.303 β = 90 c = 97.215 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 IMAGE PLATE R-AXIS IV++ mirrors 2009-05-08 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 2.34 50 98.6 0.053 27 4.7 13590 13400
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 2.34 2.42 98.3 0.347 5 4.6 1294
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.34 35.4 12702 666 98.69 0.23014 0.22775 0.2268 0.27608 0.2776 RANDOM 20.876
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] -0.46 -0.17 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.638 r_dihedral_angle_4_deg 16.323 r_dihedral_angle_3_deg 14.767 r_dihedral_angle_1_deg 5.933 r_angle_refined_deg 0.868 r_scangle_it 0.796 r_angle_other_deg 0.767 r_scbond_it 0.466 r_mcangle_it 0.358 r_symmetry_vdw_other 0.241
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.638 r_dihedral_angle_4_deg 16.323 r_dihedral_angle_3_deg 14.767 r_dihedral_angle_1_deg 5.933 r_angle_refined_deg 0.868 r_scangle_it 0.796 r_angle_other_deg 0.767 r_scbond_it 0.466 r_mcangle_it 0.358 r_symmetry_vdw_other 0.241 r_symmetry_vdw_refined 0.206 r_mcbond_it 0.192 r_nbd_refined 0.186 r_nbd_other 0.175 r_nbtor_refined 0.172 r_symmetry_hbond_refined 0.129 r_xyhbond_nbd_refined 0.114 r_nbtor_other 0.086 r_chiral_restr 0.05 r_mcbond_other 0.025 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2175 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 13
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling