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Crystal structure of UbiX mutant V47S from Colwellia psychrerythraea 34H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 293 0.1 M tri-sodium citrate, pH 5.4, 0.5 M ammonium sulfate, 1.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.39 63.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.6 α = 90 b = 97.6 β = 90 c = 97.6 γ = 90
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 2013-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97952 PAL/PLS 5C (4A)
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 1.764 97.6 99.8 0.136 26.8 40.5 30802 30737 -3
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 1.764 1.86 100 0.32 13.7 39.9
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 1.764 97.6 29186 1549 99.78 0.23759 0.23658 0.2416 0.25669 0.2596 RANDOM 24.39
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.05 r_dihedral_angle_4_deg 18.725 r_dihedral_angle_3_deg 13.879 r_dihedral_angle_1_deg 6.089 r_long_range_B_other 5.545 r_long_range_B_refined 5.543 r_scangle_other 4.298 r_mcangle_other 3.253 r_mcangle_it 3.176 r_scbond_other 3.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.05 r_dihedral_angle_4_deg 18.725 r_dihedral_angle_3_deg 13.879 r_dihedral_angle_1_deg 6.089 r_long_range_B_other 5.545 r_long_range_B_refined 5.543 r_scangle_other 4.298 r_mcangle_other 3.253 r_mcangle_it 3.176 r_scbond_other 3.031 r_scbond_it 2.97 r_mcbond_it 2.276 r_mcbond_other 2.266 r_angle_refined_deg 2.229 r_angle_other_deg 0.98 r_chiral_restr 0.135 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1522 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 10
Software Software Software Name Purpose HKL-2000 data collection MERLOT phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling