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Human alanine aminotransferase 2 in complex with PLP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XI9 PDB entry 1XI9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 0.1M citric acid, 40% PEG300, 0.1M disodium hydrogen phosphate , pH 4.2, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.94 58.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.73 α = 90 b = 92.73 β = 90 c = 262.87 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD ADSC QUANTUM 315 2008-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97 Diamond I03
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 2.3 25 99.3 30795
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36
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 1XI9 2.3 19.73 29051 1529 100 0.19189 0.18944 0.23767 0.2402 RANDOM 28.949
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 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.436 r_dihedral_angle_4_deg 21.084 r_dihedral_angle_3_deg 14.216 r_dihedral_angle_1_deg 6.686 r_scangle_it 4.266 r_scbond_it 2.988 r_mcangle_it 1.925 r_angle_refined_deg 1.761 r_mcbond_it 1.37 r_angle_other_deg 0.994
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.436 r_dihedral_angle_4_deg 21.084 r_dihedral_angle_3_deg 14.216 r_dihedral_angle_1_deg 6.686 r_scangle_it 4.266 r_scbond_it 2.988 r_mcangle_it 1.925 r_angle_refined_deg 1.761 r_mcbond_it 1.37 r_angle_other_deg 0.994 r_symmetry_vdw_other 0.282 r_mcbond_other 0.254 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.229 r_nbd_other 0.193 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.181 r_symmetry_hbond_refined 0.129 r_chiral_restr 0.102 r_nbtor_other 0.092 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3570 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 25
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling