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Crystal structure of the DAP BII
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WOK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.5 293 18% PEG8000, 20% Glycerol, 2mM ZnCl2, 80mM CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.7 54.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.46 α = 90 b = 130.71 β = 90 c = 170.47 γ = 90
Symmetry Space Group P 21 21 21
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 315r 2012-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.00000 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 2.2 30 98.6 81815
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3WOK 2.2 29.59 81788 4318 98.51 0.16773 0.16502 0.22003 0.2202 RANDOM 20.434
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] -0.15 -0.17 0.32
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.268 r_long_range_B_other 5.216 r_scangle_other 4.431 r_scbond_it 2.873 r_scbond_other 2.873 r_mcangle_other 2.512 r_mcangle_it 2.511 r_angle_refined_deg 1.836 r_mcbond_it 1.66 r_mcbond_other 1.655
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.268 r_long_range_B_other 5.216 r_scangle_other 4.431 r_scbond_it 2.873 r_scbond_other 2.873 r_mcangle_other 2.512 r_mcangle_it 2.511 r_angle_refined_deg 1.836 r_mcbond_it 1.66 r_mcbond_other 1.655 r_angle_other_deg 0.895 r_chiral_restr 0.104 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 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 10762 Nucleic Acid Atoms Solvent Atoms 908 Heterogen Atoms 45
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling