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Crystal structure of Acostatin from Agkistrodon Contortrix Contortrix
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J2L PDB ENTRY 1J2L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 1.8M AMMONIUM SULFATE, 0.1M TRIS-HCL, VAPOR DIFFUSION,
HANGING DROP, TEMPERATURE 298K, pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.48 50.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.449 α = 90 b = 59.808 β = 90 c = 121.307 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 210 2002-10-19 M SINGLE WAVELENGTH 2 1 CCD ADSC QUANTUM 210 3 1 IMAGE PLATE MAR scanner 345 mm plate 4 1 IMAGE PLATE MAR scanner 345 mm plate
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 ALS 5.0.2 2 SYNCHROTRON NSLS BEAMLINE X6A NSLS X6A 3 SYNCHROTRON SSRL BEAMLINE BL9-1 SSRL BL9-1 4 SYNCHROTRON SSRL BEAMLINE BL7-1 SSRL BL7-1
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 1.7 20 98.8 0.044 13.1 13.7 30457
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) 1.7 1.76 90.9 0.156 8.5 9.2
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 THROUGHOUT PDB ENTRY 1J2L 1.7 19.67 30750 28838 1543 98.8 0.188 0.186 0.188 0.215 0.2161 RANDOM 26.54
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 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.829 r_dihedral_angle_4_deg 13.305 r_dihedral_angle_3_deg 11.962 r_dihedral_angle_1_deg 5.883 r_scangle_it 4.755 r_scbond_it 2.959 r_mcangle_it 1.851 r_angle_refined_deg 1.329 r_mcbond_it 1.16 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.829 r_dihedral_angle_4_deg 13.305 r_dihedral_angle_3_deg 11.962 r_dihedral_angle_1_deg 5.883 r_scangle_it 4.755 r_scbond_it 2.959 r_mcangle_it 1.851 r_angle_refined_deg 1.329 r_mcbond_it 1.16 r_nbtor_refined 0.295 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.153 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 1686 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 15
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing