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Alanine-glyoxylate aminotransferase variant K390A in complex with the TPR domain of human Pex5p
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R9A PDB ENTRY 3R9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.3 293 0.1 M Bis-Tris (pH=5.3), 0.12 M LiSO4, 17% (w/w) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.556 α = 87.23 b = 74.83 β = 83.41 c = 91.751 γ = 89.83
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 MAR CCD 165 mm 2011-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.812 EMBL/DESY, HAMBURG X13
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 2.2 51.03 0.114 2.6 73170
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 PDB ENTRY 3R9A 2.2 19.74 71036 3747 96.99 0.17738 0.17526 0.21753 0.1858 RANDOM 29.249
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] 0.58 0.99 -0.07 -0.36 0.72 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.354 r_dihedral_angle_4_deg 19.35 r_dihedral_angle_3_deg 15.272 r_dihedral_angle_1_deg 5.551 r_angle_refined_deg 1.245 r_angle_other_deg 0.846 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_bond_other_d 0.005 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.354 r_dihedral_angle_4_deg 19.35 r_dihedral_angle_3_deg 15.272 r_dihedral_angle_1_deg 5.551 r_angle_refined_deg 1.245 r_angle_other_deg 0.846 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 10422 Nucleic Acid Atoms Solvent Atoms 709 Heterogen Atoms 86
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling