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Crystal structure of Hydrazidase S179A mutant complexed with a substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.1M imidazole, 0.17 M LiSO4, 2M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.66 53.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.042 α = 90 b = 126.478 β = 105.66 c = 123.185 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2013-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
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 50 97.9 0.065 29.9 3.8 196526
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 1.82 96.3 0.386 5.2 3.7
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 MOLECULAR REPLACEMENT THROUGHOUT 5H6T 1.8 40.6 186627 9889 97.63 0.17309 0.1721 0.1827 0.19158 0.202 RANDOM 18.018
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] 0.16 -0.05 -0.25 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.169 r_dihedral_angle_4_deg 16.577 r_dihedral_angle_3_deg 12.705 r_dihedral_angle_1_deg 5.878 r_long_range_B_refined 3.489 r_long_range_B_other 3.489 r_scangle_other 2.594 r_scbond_it 1.633 r_scbond_other 1.633 r_mcangle_it 1.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.169 r_dihedral_angle_4_deg 16.577 r_dihedral_angle_3_deg 12.705 r_dihedral_angle_1_deg 5.878 r_long_range_B_refined 3.489 r_long_range_B_other 3.489 r_scangle_other 2.594 r_scbond_it 1.633 r_scbond_other 1.633 r_mcangle_it 1.527 r_mcangle_other 1.527 r_angle_refined_deg 1.36 r_angle_other_deg 0.97 r_mcbond_it 0.97 r_mcbond_other 0.97 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13737 Nucleic Acid Atoms Solvent Atoms 727 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing