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Crystal structure of the soluble domain of membrane protein implicated in regulation of membrane protease activity from Corynebacterium glutamicum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.05 M Zinc acetate dihydrate, 20% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.04 39.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.546 α = 90 b = 53.084 β = 90 c = 64.357 γ = 90
Symmetry Space Group I 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 CCD ADSC QUANTUM 315 Mirrors 2008-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9793 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.65 40 98.6 0.113 13.6 6.6 9137 9137 20.43
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 1.65 1.68 86.3 0.436 2.22 2.2
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 SAD THROUGHOUT 1.65 33.2 8534 8534 428 98.57 0.17372 0.17174 0.1718 0.21594 0.2175 RANDOM 24.127
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] -1.48 1.3 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.51 r_dihedral_angle_4_deg 19.681 r_dihedral_angle_3_deg 13.264 r_dihedral_angle_1_deg 6.593 r_scangle_it 4.792 r_scbond_it 3.018 r_mcangle_it 2.054 r_angle_refined_deg 1.707 r_mcbond_it 1.246 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.51 r_dihedral_angle_4_deg 19.681 r_dihedral_angle_3_deg 13.264 r_dihedral_angle_1_deg 6.593 r_scangle_it 4.792 r_scbond_it 3.018 r_mcangle_it 2.054 r_angle_refined_deg 1.707 r_mcbond_it 1.246 r_nbtor_refined 0.304 r_nbd_refined 0.234 r_symmetry_vdw_refined 0.219 r_xyhbond_nbd_refined 0.19 r_symmetry_hbond_refined 0.154 r_chiral_restr 0.132 r_symmetry_metal_ion_refined 0.096 r_metal_ion_refined 0.019 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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_other r_symmetry_vdw_other r_symmetry_hbond_other 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 472 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MLPHARE phasing DM phasing SHELXD phasing RESOLVE phasing Coot model building