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Crystal structure of effector binding domain of central glycolytic gene regulator (CggR) from Bacillus subtilis in complex with dihydroxyacetone phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OKG PDB entry 2OKG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 298 Reservoir: 0.2M Ammonium formate pH 6.6, 20% (w/v) PEG 3350. 25mg/ml protein with 10mM glyceraldehyde-3-phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.4 48.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.537 α = 90 b = 83.822 β = 90 c = 113.712 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 IMAGE PLATE RIGAKU RAXIS IV 2007-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ DW 1.54178
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 1.8 35.9 99.2 0.06 38.7 4.9 49172 -3 33.1
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 1.8 1.86 95.6 0.51 2.1 2.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2OKG 1.8 35.9 47018 2517 99.02 0.17899 0.17703 0.21538 0.269 RANDOM 31.328
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] 0.34 -0.81 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.744 r_dihedral_angle_4_deg 13.041 r_dihedral_angle_3_deg 12.699 r_dihedral_angle_1_deg 5.028 r_scangle_it 3.139 r_scbond_it 1.922 r_angle_refined_deg 1.234 r_mcangle_it 1.028 r_mcbond_it 0.644 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.744 r_dihedral_angle_4_deg 13.041 r_dihedral_angle_3_deg 12.699 r_dihedral_angle_1_deg 5.028 r_scangle_it 3.139 r_scbond_it 1.922 r_angle_refined_deg 1.234 r_mcangle_it 1.028 r_mcbond_it 0.644 r_nbtor_refined 0.299 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined 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 3786 Nucleic Acid Atoms Solvent Atoms 603 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing