☰ Navigation Tabs
Crystal structure of Hydrazidase from Microbacterium sp. strain HM58-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.1 M imidazole, 0.17 M LiSO4, 2 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 3.02 59.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.162 α = 90 b = 128.068 β = 90 c = 159.304 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 95 CCD ADSC QUANTUM 210r 2012-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
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 1.6 50 99.9 0.054 47.2 6.1 163385
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 1.6 1.63 100 0.232 8.9 5.9
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 3H0L 1.6 33.97 155116 8193 99.68 0.16551 0.16485 0.1779 0.17809 0.1896 RANDOM 14.388
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 0.5 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.308 r_dihedral_angle_4_deg 15.321 r_dihedral_angle_3_deg 12.285 r_dihedral_angle_1_deg 5.795 r_long_range_B_refined 3.395 r_long_range_B_other 3.336 r_scangle_other 2.401 r_scbond_it 1.532 r_scbond_other 1.532 r_angle_refined_deg 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.308 r_dihedral_angle_4_deg 15.321 r_dihedral_angle_3_deg 12.285 r_dihedral_angle_1_deg 5.795 r_long_range_B_refined 3.395 r_long_range_B_other 3.336 r_scangle_other 2.401 r_scbond_it 1.532 r_scbond_other 1.532 r_angle_refined_deg 1.39 r_mcangle_it 1.259 r_mcangle_other 1.259 r_angle_other_deg 0.971 r_mcbond_it 0.78 r_mcbond_other 0.779 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 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 7040 Nucleic Acid Atoms Solvent Atoms 668 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MoRDa phasing