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1.60 Angstrom resolution crystal structure of an arginine repressor from Vibrio vulnificus CMCP6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XXB 1XXB and 1F9N experimental model PDB 1F9N 1XXB and 1F9N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 protein: 7.3 mg/mL in 10 mM Tris-HCl pH 8.3, 0.25 M NaCl, 5 mM BME. Crystallization: The Classics II Suite (A9: 0.1 M Bis-Tris pH 5.5, 3 M NaCl). Cryo: 5M NaCl+50% sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.31 46.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.308 α = 90 b = 73.308 β = 90 c = 118.597 γ = 120
Symmetry Space Group P 63 2 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 MARMOSAIC 300 mm CCD mirror 2011-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97903 APS 21-ID-D
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 1.6 30 100 0.063 38.3 14 25607 25607 -3 21.1
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 1.6 1.63 100 0.514 6.25 14.3 1242
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 (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 1XXB and 1F9N 1.6 29.65 24257 24257 1300 99.96 0.18246 0.18164 0.1969 0.19787 0.2104 RANDOM 23.941
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] -0.83 -0.41 -0.83 1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.386 r_dihedral_angle_4_deg 12.64 r_dihedral_angle_3_deg 5.87 r_scangle_it 3.408 r_scbond_it 2.021 r_angle_refined_deg 1.602 r_dihedral_angle_1_deg 1.521 r_mcangle_it 1.244 r_angle_other_deg 0.936 r_mcbond_it 0.649
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.386 r_dihedral_angle_4_deg 12.64 r_dihedral_angle_3_deg 5.87 r_scangle_it 3.408 r_scbond_it 2.021 r_angle_refined_deg 1.602 r_dihedral_angle_1_deg 1.521 r_mcangle_it 1.244 r_angle_other_deg 0.936 r_mcbond_it 0.649 r_mcbond_other 0.152 r_chiral_restr 0.094 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1118 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling