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Crystal structure of the ATP/Mg2+ bound composite dimer of HlyB-NBD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MT0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 277 Sodium acetate, isopropanol, PEG-MME 5500, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.3 45.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.926 α = 90 b = 194.917 β = 110.68 c = 63.706 γ = 90
Symmetry Space Group P 1 21 1
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 MARRESEARCH 2004-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.5 95.35 99.38 0.053 23.4 6.8 33496 33295 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 99.8 0.401 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1MT0 2.5 20 2.8 34986 33295 1761 99.38 0.22177 0.22177 0.21944 0.26426 0.2915 RANDOM 51.109
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] -0.41 -0.4 3.05 -2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.954 r_dihedral_angle_4_deg 19.36 r_dihedral_angle_3_deg 17.188 r_dihedral_angle_1_deg 5.218 r_angle_refined_deg 1.037 r_scangle_it 0.507 r_mcangle_it 0.425 r_nbtor_refined 0.295 r_scbond_it 0.276 r_mcbond_it 0.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.954 r_dihedral_angle_4_deg 19.36 r_dihedral_angle_3_deg 17.188 r_dihedral_angle_1_deg 5.218 r_angle_refined_deg 1.037 r_scangle_it 0.507 r_mcangle_it 0.425 r_nbtor_refined 0.295 r_scbond_it 0.276 r_mcbond_it 0.235 r_nbd_refined 0.179 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.108 r_metal_ion_refined 0.092 r_symmetry_hbond_refined 0.086 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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_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 7552 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing