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Crystal structure of had family enzyme bt-2542 from bacteroides thetaiotaomicron (target efi-501088)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I6X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 1.6M SODIUM ACETATE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.33 47.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.252 α = 90 b = 75.424 β = 90 c = 131.27 γ = 90
Symmetry Space Group I 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 CCD ADSC QUANTUM 315 MIRRORS 2011-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 1.64 70 98.6 0.1 7.8 9.8 30924 -5 27.213
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 1.64 1.67 98.1 0.9 1.2 7.6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR THROUGHOUT 2I6X 1.65 50 29399 962 99.61 0.1774 0.17632 0.1773 0.21016 0.208 RANDOM 38.748
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] -0.7 3.15 -2.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.288 r_dihedral_angle_3_deg 13.704 r_dihedral_angle_4_deg 11.44 r_scangle_it 10.339 r_scbond_it 6.909 r_dihedral_angle_1_deg 5.38 r_mcangle_it 4.845 r_mcbond_it 3.279 r_angle_refined_deg 1.304 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.288 r_dihedral_angle_3_deg 13.704 r_dihedral_angle_4_deg 11.44 r_scangle_it 10.339 r_scbond_it 6.909 r_dihedral_angle_1_deg 5.38 r_mcangle_it 4.845 r_mcbond_it 3.279 r_angle_refined_deg 1.304 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 1656 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 11
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling