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Crystal structure of Aplysia ACHBP in complex with 4-0H-DMXBA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BYN PDB ENTRY 2BYN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 26% PEG400, 0.1 M HEPES, PH 7.5, 0.2 M MGCL2
Crystal Properties Matthews coefficient Solvent content 2.62 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.909 α = 90 b = 115.394 β = 90 c = 130.607 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 100 CCD ADSC CCD 2005-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 56.8 99.9 0.05 20.7 6.5 132537 24.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.84 100 0.39 4.5 6.4
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 PDB ENTRY 2BYN 1.75 20 125779 6584 99.91 0.17131 0.16965 0.1923 0.20308 0.2197 RANDOM 32.431
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] 1.08 -0.73 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.14 r_dihedral_angle_4_deg 20.581 r_dihedral_angle_3_deg 14.029 r_dihedral_angle_1_deg 6.11 r_scangle_it 4.548 r_scbond_it 3.091 r_mcangle_it 2.828 r_mcbond_it 2.036 r_angle_refined_deg 1.489 r_angle_other_deg 0.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.14 r_dihedral_angle_4_deg 20.581 r_dihedral_angle_3_deg 14.029 r_dihedral_angle_1_deg 6.11 r_scangle_it 4.548 r_scbond_it 3.091 r_mcangle_it 2.828 r_mcbond_it 2.036 r_angle_refined_deg 1.489 r_angle_other_deg 0.808 r_mcbond_other 0.619 r_symmetry_vdw_other 0.24 r_symmetry_hbond_refined 0.232 r_nbd_other 0.195 r_nbd_refined 0.193 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.147 r_symmetry_vdw_refined 0.091 r_chiral_restr 0.09 r_nbtor_other 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8406 Nucleic Acid Atoms Solvent Atoms 780 Heterogen Atoms 185
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing