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Crystal structure of apaG Protein from Vibrio cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TZA pdb entry 1TZA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Bis-Tris, Magnesium, Formate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.54 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.138 α = 90 b = 67.998 β = 131.43 c = 64.002 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 CUSTOM-MADE 2004-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97940 APS 19-ID
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 2.01 50 94.7 0.112 6.1 19199 18181
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 2.01 2.1 77.2 0.267 5.6 5
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 MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1TZA 2.01 48 17250 17250 931 93.77 0.18426 0.18426 0.17997 0.1832 0.26585 0.2692 RANDOM 26.312
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] 5.21 3.77 -2.22 2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.697 r_dihedral_angle_4_deg 25.197 r_dihedral_angle_3_deg 18.698 r_dihedral_angle_1_deg 7.36 r_scangle_it 7.326 r_scbond_it 5.093 r_angle_refined_deg 2.749 r_mcangle_it 2.558 r_mcbond_it 1.79 r_nbtor_refined 0.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.697 r_dihedral_angle_4_deg 25.197 r_dihedral_angle_3_deg 18.698 r_dihedral_angle_1_deg 7.36 r_scangle_it 7.326 r_scbond_it 5.093 r_angle_refined_deg 2.749 r_mcangle_it 2.558 r_mcbond_it 1.79 r_nbtor_refined 0.329 r_nbd_refined 0.284 r_xyhbond_nbd_refined 0.229 r_symmetry_vdw_refined 0.226 r_symmetry_hbond_refined 0.213 r_chiral_restr 0.212 r_bond_refined_d 0.038 r_gen_planes_refined 0.014 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1972 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing