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Crystal structure of CTX A2 from Taiwan Cobra (Naja naja atra)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BHI PDB ENTRY 2BHI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 291 5.5 M ammonium nitrate, 0.1 M Bis-Tris, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 4.28 71.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.412 α = 90 b = 107.412 β = 90 c = 100.256 γ = 90
Symmetry Space Group P 43 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 200 CCD ADSC QUANTUM 315 2009-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1 NSRRC BL13B1
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 2.74 30 99.9 0.103 13.2 15.5 15886 15865 2 2
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 2.74 2.84 100 0.494 15
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 2BHI 2.74 25.62 15886 15030 792 99.58 0.19979 0.1966 0.1996 0.2596 0.2536 RANDOM 44.846
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] -2.31 -2.31 4.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.63 r_dihedral_angle_4_deg 24.847 r_dihedral_angle_3_deg 23.129 r_dihedral_angle_1_deg 7.743 r_mcangle_it 5.152 r_scbond_it 3.746 r_mcbond_it 3.368 r_mcbond_other 3.36 r_angle_refined_deg 1.914 r_angle_other_deg 0.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.63 r_dihedral_angle_4_deg 24.847 r_dihedral_angle_3_deg 23.129 r_dihedral_angle_1_deg 7.743 r_mcangle_it 5.152 r_scbond_it 3.746 r_mcbond_it 3.368 r_mcbond_other 3.36 r_angle_refined_deg 1.914 r_angle_other_deg 0.877 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2325 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing