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Crystal structure of gamma-butyrolactone receptor (ArpA-like protein)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UI5 PDB ENTRY 1UI5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 PEG 6000, lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.792 α = 90 b = 69.562 β = 90 c = 148.933 γ = 90
Symmetry Space Group P 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 4 2001-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0 Photon Factory BL-6A
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 2 30 92.8 0.047 0.047 9 4.4 31849 31849 31.5
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 2 2.11 91.6 0.205 0.205 3.4 3.4 3591
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1UI5 2.4 30 15231 13950 751 91.59 0.22787 0.22787 0.22493 0.2272 0.28401 0.2774 RANDOM 21.86
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] 2.08 -0.68 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.09 r_scangle_it 4.705 r_dihedral_angle_1_deg 3.264 r_scbond_it 2.694 r_mcangle_it 1.668 r_angle_refined_deg 1.573 r_mcbond_it 0.874 r_angle_other_deg 0.818 r_symmetry_hbond_refined 0.297 r_symmetry_vdw_refined 0.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.09 r_scangle_it 4.705 r_dihedral_angle_1_deg 3.264 r_scbond_it 2.694 r_mcangle_it 1.668 r_angle_refined_deg 1.573 r_mcbond_it 0.874 r_angle_other_deg 0.818 r_symmetry_hbond_refined 0.297 r_symmetry_vdw_refined 0.278 r_nbd_refined 0.26 r_nbd_other 0.219 r_symmetry_vdw_other 0.196 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.085 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_xyhbond_nbd_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3025 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing