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The crystal structure of a putative aminotransferase from Corynebacterium diphtheriae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.2M NH4Cl
20% (w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.29 46.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.248 α = 90 b = 56.081 β = 102.47 c = 173.592 γ = 90
Symmetry Space Group P 1 21 1
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 QUANTUM 315 Mirror 2007-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97943 APS 19-ID
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 42.7 86.9 0.084 12 2.9 99497 99497
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 64.7 0.377 1.45 2.5 7337
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 2 42.68 97821 97821 5228 90.42 0.19249 0.19249 0.18992 0.1912 0.24093 0.2419 RANDOM 36.29
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] 0.17 -0.09 -0.22 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.803 r_dihedral_angle_3_deg 17.852 r_dihedral_angle_4_deg 15.141 r_dihedral_angle_1_deg 6.314 r_scangle_it 2.766 r_scbond_it 2 r_angle_refined_deg 1.546 r_mcangle_it 1.092 r_mcbond_it 0.736 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.803 r_dihedral_angle_3_deg 17.852 r_dihedral_angle_4_deg 15.141 r_dihedral_angle_1_deg 6.314 r_scangle_it 2.766 r_scbond_it 2 r_angle_refined_deg 1.546 r_mcangle_it 1.092 r_mcbond_it 0.736 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.193 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.11 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12609 Nucleic Acid Atoms Solvent Atoms 683 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling SHELXD phasing MLPHARE phasing DM phasing RESOLVE phasing HKL-3000 phasing