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Crystal structure of the DAP BII (Space)
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 COUNTER-DIFFUSION 9.5 293 18% PEG8000, 20% Glycerol, 2mM ZnCl2, 80mM CHES, pH 9.5, Counter-diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.7 54.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.74 α = 90 b = 130.44 β = 90 c = 171.46 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 RAYONIX MX225HE 2011-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.80000 SPring-8 BL41XU
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 1.95 30 99 117965 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 1.95 29.56 117940 6223 98.65 0.18396 0.18178 0.1884 0.22531 0.2268 RANDOM 20.887
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 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.667 r_long_range_B_other 5.495 r_scangle_other 3.997 r_scbond_it 2.563 r_scbond_other 2.562 r_mcangle_it 2.401 r_mcangle_other 2.401 r_angle_refined_deg 1.889 r_mcbond_it 1.629 r_mcbond_other 1.626
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.667 r_long_range_B_other 5.495 r_scangle_other 3.997 r_scbond_it 2.563 r_scbond_other 2.562 r_mcangle_it 2.401 r_mcangle_other 2.401 r_angle_refined_deg 1.889 r_mcbond_it 1.629 r_mcbond_other 1.626 r_angle_other_deg 0.91 r_chiral_restr 0.105 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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 10760 Nucleic Acid Atoms Solvent Atoms 1257 Heterogen Atoms 70
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling