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Crystal structure of the DAP BII dipeptide complex I
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 Val-Tyr, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.86 α = 90 b = 121.86 β = 90 c = 219.41 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 2013-05-19 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 1.74 30 98.4 168682 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 1.74 29.56 157501 8341 98.29 0.19416 0.19183 0.1989 0.23854 0.2423 RANDOM 26.066
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 6.099 r_long_range_B_other 6.015 r_scangle_other 4.525 r_mcangle_it 2.994 r_mcangle_other 2.994 r_scbond_it 2.986 r_scbond_other 2.986 r_mcbond_it 2.155 r_mcbond_other 2.155 r_angle_refined_deg 1.826
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 6.099 r_long_range_B_other 6.015 r_scangle_other 4.525 r_mcangle_it 2.994 r_mcangle_other 2.994 r_scbond_it 2.986 r_scbond_other 2.986 r_mcbond_it 2.155 r_mcbond_other 2.155 r_angle_refined_deg 1.826 r_angle_other_deg 0.91 r_chiral_restr 0.112 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 10734 Nucleic Acid Atoms Solvent Atoms 1270 Heterogen Atoms 81
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling