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Structure of the zinc transporter YiiP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 5.856 78.998
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.66 α = 90 b = 110.839 β = 90 c = 130.662 γ = 90
Symmetry Space Group P 2 2 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 MAR CCD 165 mm 2006-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.0 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.8 30 97.3 0.129 0.129 13.3 6 16000 15534 2 2 100
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.8 4 91.9 0.429 0.429 1.9 3 1000
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MIR THROUGHOUT 3.8 12 16000 14484 775 100 0.32259 0.32223 0.3481 0.32934 0.3325 RANDOM 116.019
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] 10.48 3.47 -13.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.903 r_dihedral_angle_3_deg 26.532 r_dihedral_angle_4_deg 18.424 r_dihedral_angle_1_deg 15.721 r_mcangle_it 3.236 r_scangle_it 2.924 r_angle_refined_deg 2.834 r_mcbond_it 1.794 r_scbond_it 1.643 r_symmetry_vdw_refined 0.448
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.903 r_dihedral_angle_3_deg 26.532 r_dihedral_angle_4_deg 18.424 r_dihedral_angle_1_deg 15.721 r_mcangle_it 3.236 r_scangle_it 2.924 r_angle_refined_deg 2.834 r_mcbond_it 1.794 r_scbond_it 1.643 r_symmetry_vdw_refined 0.448 r_symmetry_metal_ion_refined 0.445 r_symmetry_hbond_refined 0.398 r_nbd_refined 0.384 r_nbtor_refined 0.347 r_xyhbond_nbd_refined 0.329 r_metal_ion_refined 0.265 r_chiral_restr 0.214 r_bond_refined_d 0.027 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4410 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALA data scaling SHARP phasing