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Crystal structure of a putative aminotransferase from Silicibacter pomeroyi
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 200mM Calcium acetate, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.17 43.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.367 α = 90 b = 86.376 β = 90 c = 144.325 γ = 90
Symmetry Space Group C 2 2 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 CCD MAR CCD 165 mm 2009-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97929 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 21.81 99.9 0.098 17 14.6 29683 19.559
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 100 0.489 6.7 14.6 4287
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.9 21.81 29645 1503 100 0.192 0.189 0.238 0.254 RANDOM 25.844
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 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.752 r_dihedral_angle_4_deg 14.663 r_dihedral_angle_3_deg 13.022 r_dihedral_angle_1_deg 5.445 r_scangle_it 3.57 r_scbond_it 2.694 r_angle_refined_deg 1.497 r_mcangle_it 1.369 r_mcbond_it 1.165 r_angle_other_deg 0.971
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.752 r_dihedral_angle_4_deg 14.663 r_dihedral_angle_3_deg 13.022 r_dihedral_angle_1_deg 5.445 r_scangle_it 3.57 r_scbond_it 2.694 r_angle_refined_deg 1.497 r_mcangle_it 1.369 r_mcbond_it 1.165 r_angle_other_deg 0.971 r_symmetry_hbond_refined 0.291 r_symmetry_vdw_other 0.264 r_mcbond_other 0.251 r_nbd_refined 0.218 r_nbd_other 0.194 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.136 r_symmetry_vdw_refined 0.12 r_nbtor_other 0.088 r_chiral_restr 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2727 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SCALA data scaling HKL2Map phasing