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Sugar transaminase from Archaeoglobus veneficus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.2 291 0.1 M phosphate/citrate
20 % w/v PEG 6K
Crystal Properties Matthews coefficient Solvent content 2.26 45.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.227 α = 90 b = 105.953 β = 90 c = 111.216 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 PIXEL DECTRIS PILATUS 2M 2013-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.27 49.29 97.7 0.04 1 17.3 5 212879
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.27 1.29 87 1.352 0.305 0.9 3.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3nyu 1.27 49.287 212778 10625 97.585 0.153 0.1516 0.1516 0.1747 0.1746 21.446
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] -0.31 0.078 0.232
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.117 r_dihedral_angle_4_deg 17.695 r_dihedral_angle_3_deg 14.353 r_lrange_it 7.875 r_lrange_other 7.871 r_scangle_it 6.622 r_scangle_other 6.554 r_dihedral_angle_1_deg 6.167 r_scbond_it 4.894 r_scbond_other 4.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.117 r_dihedral_angle_4_deg 17.695 r_dihedral_angle_3_deg 14.353 r_lrange_it 7.875 r_lrange_other 7.871 r_scangle_it 6.622 r_scangle_other 6.554 r_dihedral_angle_1_deg 6.167 r_scbond_it 4.894 r_scbond_other 4.79 r_mcangle_other 3.759 r_mcangle_it 3.758 r_mcbond_it 2.673 r_mcbond_other 2.65 r_angle_refined_deg 1.665 r_angle_other_deg 1.377 r_nbd_refined 0.22 r_nbd_other 0.203 r_xyhbond_nbd_refined 0.189 r_symmetry_nbd_other 0.179 r_symmetry_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.172 r_symmetry_nbd_refined 0.162 r_xyhbond_nbd_other 0.158 r_ncsr_local_group_1 0.117 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5982 Nucleic Acid Atoms Solvent Atoms 725 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MoRDa phasing Coot model building