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Crystal structure of putative aminotransferase (YP_614685.1) from SILICIBACTER SP. TM1040 at 1.80 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 277 30.0000% PEG-6000, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.14 42.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.85 α = 90 b = 96.25 β = 105.51 c = 60.3 γ = 90
Symmetry Space Group C 1 2 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 MARMOSAIC 300 mm CCD ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY 2008-10-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.94645,0.97962 APS 23-ID-B
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 1.8 29.44 91.8 0.061 9.36 37793 -3 22.63
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 1.8 1.86 91.3 0.648 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.8 29.44 37767 1896 96.5 0.208 0.205 0.2076 0.254 0.2529 RANDOM 26.22
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] -1.46 0.65 -2.06 3.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.163 r_dihedral_angle_4_deg 15.294 r_dihedral_angle_3_deg 12.074 r_dihedral_angle_1_deg 4.024 r_mcangle_it 1.757 r_scangle_it 1.741 r_angle_refined_deg 1.737 r_mcbond_it 1.278 r_scbond_it 1.168 r_angle_other_deg 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.163 r_dihedral_angle_4_deg 15.294 r_dihedral_angle_3_deg 12.074 r_dihedral_angle_1_deg 4.024 r_mcangle_it 1.757 r_scangle_it 1.741 r_angle_refined_deg 1.737 r_mcbond_it 1.278 r_scbond_it 1.168 r_angle_other_deg 1.06 r_mcbond_other 0.295 r_symmetry_vdw_refined 0.216 r_symmetry_hbond_refined 0.214 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.193 r_nbd_other 0.191 r_symmetry_vdw_other 0.186 r_nbtor_refined 0.178 r_chiral_restr 0.106 r_nbtor_other 0.088 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3509 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing