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Structure of Deinococcus radiodurans N-acylamino acid racemase at 1.3 : insights into a flexible binding pocket and evolution of enzymatic activity
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 45.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.367 α = 90 b = 116.367 β = 90 c = 120.467 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 123 IMAGE PLATE RIGAKU RAXIS M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 1.0093, 1.0085, 0.9924, 1.5418 SPring-8 BL12B2
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 1.3 30 99.9 0.08 25.5 391835 5
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) 1.3 1.35 99 41.5 0.08 4.96 391835
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 (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 MAD THROUGHOUT 1.3 30 371660 19678 0.1553 0.1553 0.15436 0.1744 0.17299 0.1854 RANDOM 12.123
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] 0.22 0.22 -0.44
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 7.048 r_dihedral_angle_1_deg 5.914 r_sphericity_bonded 2.746 r_scangle_it 2.537 r_mcangle_it 1.995 r_scbond_it 1.671 r_mcbond_it 1.34 r_angle_refined_deg 1.281 r_angle_other_deg 0.73 r_rigid_bond_restr 0.554
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 7.048 r_dihedral_angle_1_deg 5.914 r_sphericity_bonded 2.746 r_scangle_it 2.537 r_mcangle_it 1.995 r_scbond_it 1.671 r_mcbond_it 1.34 r_angle_refined_deg 1.281 r_angle_other_deg 0.73 r_rigid_bond_restr 0.554 r_symmetry_vdw_other 0.292 r_nbd_other 0.268 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.202 r_symmetry_hbond_refined 0.2 r_nbtor_other 0.084 r_chiral_restr 0.075 r_gen_planes_other 0.012 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11064 Nucleic Acid Atoms Solvent Atoms 1667 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing REFMAC refinement