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Crystal structure of the ATPase domain of TAP1 with ATP (D645Q, Q678H mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IXE PDB ENTRY 2IXE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 HANGING DROP VAPOR DIFFUSION WITH THE RESERVOIR CONTAINING 0.75 M TRI-SODIUM CITRATE PH 8.0 .
Crystal Properties Matthews coefficient Solvent content 2.35 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.269 α = 90 b = 108.917 β = 90 c = 123.561 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 277 IMAGE PLATE RIGAKU IMAGE PLATE MIRRORS 2006-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 2 40 98.9 0.08 18.1 4.4 74956 2
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 2 2.07 100 0.5 3.3 4.3
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 2IXE 2 38.49 71102 3776 98.8 0.218 0.216 0.218 0.258 0.2612 RANDOM 29.56
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] -1.21 -0.13 1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.701 r_dihedral_angle_4_deg 13.671 r_dihedral_angle_3_deg 13.52 r_dihedral_angle_1_deg 5.146 r_scangle_it 1.375 r_angle_refined_deg 1.097 r_angle_other_deg 0.911 r_scbond_it 0.891 r_mcangle_it 0.526 r_mcbond_it 0.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.701 r_dihedral_angle_4_deg 13.671 r_dihedral_angle_3_deg 13.52 r_dihedral_angle_1_deg 5.146 r_scangle_it 1.375 r_angle_refined_deg 1.097 r_angle_other_deg 0.911 r_scbond_it 0.891 r_mcangle_it 0.526 r_mcbond_it 0.453 r_nbd_refined 0.184 r_symmetry_vdw_other 0.178 r_nbd_other 0.172 r_nbtor_refined 0.166 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.136 r_symmetry_vdw_refined 0.11 r_nbtor_other 0.081 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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_mcbond_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 7631 Nucleic Acid Atoms Solvent Atoms 968 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing