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Crystal structure of permease family protein from Vibrio cholerae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.2M Potassium iodide, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.31 46.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.914 α = 90 b = 90.914 β = 90 c = 65.21 γ = 90
Symmetry Space Group P 4 21 2
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 2010-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97937 APS 19-ID
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 2.25 50 99.9 0.096 63.7 13.7 13528 13508 -3 44.6
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) 2.25 2.29 100 0.503 12.2 14.5 656
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 2.25 50 13300 13300 642 98.45 0.1957 0.1957 0.19316 0.2311 0.24745 0.2514 RANDOM 28.258
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] 0.14 0.14 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.62 r_dihedral_angle_4_deg 17.413 r_dihedral_angle_3_deg 15.753 r_dihedral_angle_1_deg 5.082 r_scangle_it 4.348 r_scbond_it 2.665 r_mcangle_it 1.437 r_angle_refined_deg 1.278 r_rigid_bond_restr 1.268 r_mcbond_it 0.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.62 r_dihedral_angle_4_deg 17.413 r_dihedral_angle_3_deg 15.753 r_dihedral_angle_1_deg 5.082 r_scangle_it 4.348 r_scbond_it 2.665 r_mcangle_it 1.437 r_angle_refined_deg 1.278 r_rigid_bond_restr 1.268 r_mcbond_it 0.782 r_chiral_restr 0.077 r_bond_refined_d 0.013 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1975 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 11
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM model building RESOLVE model building Coot model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing RESOLVE phasing