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Crystal structure of the DAP BII dipeptide complex II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WOI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.5 293 18% PEG 8000, 20% Glycerol, 2mM ZnCl2, 80mM CHES, 2mM Angiotensin II, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.22 α = 90 b = 122.22 β = 90 c = 219.76 γ = 90
Symmetry Space Group P 43 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 95 CCD ADSC QUANTUM 270 2013-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98000 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.86 40 98.4 130273 2
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 3WOI 1.86 39.21 130273 6897 98.29 0.1854 0.18323 0.1922 0.22525 0.2331 RANDOM 27.966
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] 0.07 0.07 -0.13
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.811 r_long_range_B_other 5.757 r_scangle_other 4.83 r_scbond_it 3.243 r_scbond_other 3.239 r_mcangle_it 3.153 r_mcangle_other 3.152 r_mcbond_it 2.339 r_mcbond_other 2.339 r_angle_refined_deg 1.861
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.811 r_long_range_B_other 5.757 r_scangle_other 4.83 r_scbond_it 3.243 r_scbond_other 3.239 r_mcangle_it 3.153 r_mcangle_other 3.152 r_mcbond_it 2.339 r_mcbond_other 2.339 r_angle_refined_deg 1.861 r_angle_other_deg 0.928 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10742 Nucleic Acid Atoms Solvent Atoms 984 Heterogen Atoms 104
Software Software Software Name Purpose ADSC data collection REFMAC refinement MOSFLM data reduction SCALA data scaling