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Crystal structure of universal stress protein MSMEG_3811 in complex with cAMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z08 PDB ENTRY 2Z08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 PROTEIN WAS COCRYSTALLIZED WITH 5 MM CAMP IN 0.1 M MES, PH 6.0; 1.9 M AMMONIUM SULFATE; 6 % (V/V) POLYPROPYLENGLYCOL 400.
Crystal Properties Matthews coefficient Solvent content 2.04 39.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.53 α = 90 b = 126.78 β = 90 c = 151.72 γ = 90
Symmetry Space Group C 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 PIXEL DECTRIS PILATUS 6M COLLIMATOR 2013-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 2.15 48.64 98.8 0.08 15.1 4.5 43084 -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 2.15 2.21 98.5 0.9 1.8 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 2Z08 2.15 48.64 40929 2155 98.79 0.18158 0.17875 0.1871 0.2352 0.24 RANDOM
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 30.894 r_dihedral_angle_4_deg 19.685 r_dihedral_angle_3_deg 15.473 r_long_range_B_refined 7.419 r_long_range_B_other 7.418 r_dihedral_angle_1_deg 6.475 r_scangle_other 4.377 r_mcangle_it 3.054 r_mcangle_other 3.054 r_scbond_it 2.861
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.894 r_dihedral_angle_4_deg 19.685 r_dihedral_angle_3_deg 15.473 r_long_range_B_refined 7.419 r_long_range_B_other 7.418 r_dihedral_angle_1_deg 6.475 r_scangle_other 4.377 r_mcangle_it 3.054 r_mcangle_other 3.054 r_scbond_it 2.861 r_scbond_other 2.861 r_mcbond_it 1.967 r_mcbond_other 1.966 r_angle_refined_deg 1.901 r_angle_other_deg 0.863 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 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 5579 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 230
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling BALBES phasing