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Crystal structure of iMazG from Vibrio DAT 722: Ctag-iMazG (P41212)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q5Z PDB ENTRY 2Q5Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.05 293 0.1 M sodium citrate, 1.9 M ammonium sulfate, 500 mM NaCl, 10% 2-methyl-2,4-pentanediol, 10 mM MgCl2, 10 mM dCTP, pH 5.05, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.28 62.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.963 α = 90 b = 87.963 β = 90 c = 158.976 γ = 90
Symmetry Space Group P 41 21 2
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 MARMOSAIC 300 mm CCD SI(111) DOUBLE CRYSTAL MONOCHROMETER 2006-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.798 76.966 94.9 0.079 0.079 3.9 8.7 55795 26.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 100 0.551 0.551 1.4 7.3
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 (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 PDB ENTRY 2Q5Z 1.8 33.84 55480 55480 2778 94.5 0.203 0.201 0.2013 0.227 0.2265 RANDOM 29.83
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] -0.31 -0.31 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.443 r_dihedral_angle_3_deg 12.544 r_dihedral_angle_4_deg 9.928 r_dihedral_angle_1_deg 5.083 r_scangle_it 3.457 r_scbond_it 2.178 r_angle_refined_deg 1.263 r_mcangle_it 1.143 r_mcbond_it 0.737 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.443 r_dihedral_angle_3_deg 12.544 r_dihedral_angle_4_deg 9.928 r_dihedral_angle_1_deg 5.083 r_scangle_it 3.457 r_scbond_it 2.178 r_angle_refined_deg 1.263 r_mcangle_it 1.143 r_mcbond_it 0.737 r_nbtor_refined 0.302 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.159 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 2746 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 4
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction