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Crystal structure of the DAP BII dipeptide complex III
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 IV, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.59 52.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.05 α = 90 b = 122.05 β = 90 c = 219.37 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 0.97999 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 1.75 40 98.9 156144
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 1.75 39.11 156140 8264 98.8 0.18987 0.18779 0.1961 0.2293 0.2356 RANDOM 27.409
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]
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.647 r_long_range_B_other 5.621 r_scangle_other 4.798 r_scbond_it 3.187 r_scbond_other 3.185 r_mcangle_it 3.087 r_mcangle_other 3.087 r_mcbond_it 2.269 r_mcbond_other 2.268 r_angle_refined_deg 1.835
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.647 r_long_range_B_other 5.621 r_scangle_other 4.798 r_scbond_it 3.187 r_scbond_other 3.185 r_mcangle_it 3.087 r_mcangle_other 3.087 r_mcbond_it 2.269 r_mcbond_other 2.268 r_angle_refined_deg 1.835 r_angle_other_deg 0.918 r_chiral_restr 0.116 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 964 Heterogen Atoms 98
Software Software Software Name Purpose ADSC data collection REFMAC refinement MOSFLM data reduction SCALA data scaling