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Crystal structure of transcriptional coactivator/pterin dehydratase from Brucella Melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DCH pdb entry 1DCH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 HAMPTON CRYSTAL SCREEN HT CONDITION G6. 100 MM HEPES PH 7.5, 10% PEG 6000, 5% MPD. PROTEIN CONCENTRATION 23 MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.759 α = 90 b = 85.498 β = 90 c = 50.68 γ = 90
Symmetry Space Group P 21 21 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 RIGAKU SATURN 944+ MIRRORS 2009-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT
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 2.1 85.5 99.1 0.085 9.4 6.9 14045
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 2.1 2.14 85.7 0.233 5.6
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 1DCH 2.1 50 13998 703 0.182 0.18 0.1899 0.218 0.229 RANDOM 10.04
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] -0.31 -0.57 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.823 r_dihedral_angle_4_deg 18.615 r_dihedral_angle_3_deg 10.877 r_dihedral_angle_1_deg 5.264 r_scangle_it 2.044 r_scbond_it 1.199 r_angle_refined_deg 0.879 r_angle_other_deg 0.739 r_mcangle_it 0.69 r_mcbond_it 0.339
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.823 r_dihedral_angle_4_deg 18.615 r_dihedral_angle_3_deg 10.877 r_dihedral_angle_1_deg 5.264 r_scangle_it 2.044 r_scbond_it 1.199 r_angle_refined_deg 0.879 r_angle_other_deg 0.739 r_mcangle_it 0.69 r_mcbond_it 0.339 r_chiral_restr 0.058 r_mcbond_other 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1524 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 8
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling