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Crystal structure of the ectoine-binding protein UehA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VPO PDB entry 2VPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 278 100mM Na Citrate pH 5.6-6.0, 2.4-2.6M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63 α = 90 b = 61.3 β = 102.6 c = 86.3 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 CCD ADSC QUANTUM 315r 2008-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9000 ESRF ID23-1
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 2.9 20 99.6 0.111 11.32 4 14412 2 44.69
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 2.9 2.97 99.9 0.426 3.5 3.6
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 2VPO 2.9 19.86 13642 718 100 0.22009 0.218 0.2201 0.26161 0.2594 RANDOM 43.083
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] -0.03 0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.498 r_dihedral_angle_3_deg 17.401 r_dihedral_angle_4_deg 15.631 r_dihedral_angle_1_deg 5.07 r_angle_refined_deg 0.965 r_scangle_it 0.847 r_scbond_it 0.522 r_mcangle_it 0.387 r_nbtor_refined 0.296 r_mcbond_it 0.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.498 r_dihedral_angle_3_deg 17.401 r_dihedral_angle_4_deg 15.631 r_dihedral_angle_1_deg 5.07 r_angle_refined_deg 0.965 r_scangle_it 0.847 r_scbond_it 0.522 r_mcangle_it 0.387 r_nbtor_refined 0.296 r_mcbond_it 0.266 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.18 r_xyhbond_nbd_refined 0.105 r_chiral_restr 0.069 r_symmetry_hbond_refined 0.045 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 4862 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 20
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling