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Crystal structure of a ZN-bound histidine triad family protein from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y23 PDB entry 1Y23
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 289 JCSG A4; 30 % MPD, 0.1 M ACETATE PH 4.6, 20 MM CACL2, MYSMA.00754.A.A1 AT 19.9 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.19 43.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.15 α = 90 b = 63.52 β = 100.51 c = 76.5 γ = 90
Symmetry Space Group C 1 2 1
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 SATURN 2010-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.9 35.27 95.5 0.04 23.01 3.5 22067 21077 -3 20.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 80.5 4.9 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MR THROUGHOUT PDB entry 1Y23 1.9 35.27 22067 21053 1062 0.159 0.159 0.157 0.172 0.191 0.2073 RANDOM 14.73
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] -0.74 -0.19 1.67 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.919 r_dihedral_angle_4_deg 19.837 r_dihedral_angle_3_deg 11.911 r_dihedral_angle_1_deg 6.179 r_scangle_it 2.639 r_scbond_it 1.637 r_angle_refined_deg 1.362 r_mcangle_it 0.97 r_angle_other_deg 0.875 r_mcbond_it 0.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.919 r_dihedral_angle_4_deg 19.837 r_dihedral_angle_3_deg 11.911 r_dihedral_angle_1_deg 6.179 r_scangle_it 2.639 r_scbond_it 1.637 r_angle_refined_deg 1.362 r_mcangle_it 0.97 r_angle_other_deg 0.875 r_mcbond_it 0.529 r_mcbond_other 0.12 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2044 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 60
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling