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Crystal structure of a Rex-family transcriptional regulatory protein from Streptococcus agalactiae complexed with NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KEO PDB ENTRY 3KEO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 17% PEG 3350, 175 mM sodium fluoride, 100 mM BisTrisPropane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.67 α = 90 b = 71.47 β = 90 c = 113.88 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 MAR CCD 165 mm mirrors 2009-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.0379 MAX II I911-2
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 2.4 28.47 99.4 0.042 27.3 6 18996 18880 -3 64
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) 2.4 2.46 100 0.532 3.65 6.1 1369
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 3KEO 2.4 28.47 17958 978 99.35 0.22671 0.22329 0.2289 0.29176 0.292 RANDOM 60.852
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] -0.14 -0.01 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.211 r_dihedral_angle_4_deg 26.323 r_dihedral_angle_3_deg 19 r_dihedral_angle_1_deg 6.63 r_scangle_it 3.342 r_scbond_it 2.169 r_angle_refined_deg 1.678 r_mcangle_it 1.466 r_angle_other_deg 1.008 r_mcbond_it 0.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.211 r_dihedral_angle_4_deg 26.323 r_dihedral_angle_3_deg 19 r_dihedral_angle_1_deg 6.63 r_scangle_it 3.342 r_scbond_it 2.169 r_angle_refined_deg 1.678 r_mcangle_it 1.466 r_angle_other_deg 1.008 r_mcbond_it 0.796 r_mcbond_other 0.156 r_chiral_restr 0.096 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 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 3147 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 44
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling