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The crystal structure of the HlyB-NBD E631Q mutant in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MT0 pdb entry 1MT0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 100 mM Tris, 16% PEG 6000, 5% MPD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.08 40.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.568 α = 90 b = 34.748 β = 97.97 c = 37.518 γ = 90
Symmetry Space Group C 1 2 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 2003-08-08 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 1.9 20 94.1 0.049 16370 2.3
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 1.9 1.95 94.1 0.277 2.3 16370
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1MT0 1.9 20 2.3 16370 876 94.1 0.20403 0.20161 0.214 0.25023 0.2647 RANDOM 37.036
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] -1.79 -3.29 -1.01 1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.484 r_scangle_it 5.377 r_scbond_it 3.214 r_mcangle_it 2.95 r_mcbond_it 1.633 r_angle_refined_deg 1.414 r_angle_other_deg 0.837 r_symmetry_vdw_other 0.249 r_nbd_other 0.241 r_nbd_refined 0.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.484 r_scangle_it 5.377 r_scbond_it 3.214 r_mcangle_it 2.95 r_mcbond_it 1.633 r_angle_refined_deg 1.414 r_angle_other_deg 0.837 r_symmetry_vdw_other 0.249 r_nbd_other 0.241 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.199 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.151 r_nbtor_other 0.084 r_chiral_restr 0.081 r_bond_other_d 0.014 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1912 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing