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Crystal structure of crotoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QOG PDB ENTRY 2QOG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 290 30% PEG 4000, 0.1 M sodium acetate, 0.1 M magnesium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 1.73 28.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.664 α = 90 b = 65.309 β = 103.9 c = 37.429 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315r 2009-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 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 1.35 36.33 98.9 0.066 13.9 4.2 35132 -3 12.98
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 1.35 1.42 96.2 0.469 1.9 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2QOG 1.35 36.33 33344 1762 98.8 0.166 0.165 0.1734 0.189 0.1944 RANDOM 14.06
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] -0.07 -1.11 0.39 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.532 r_dihedral_angle_4_deg 16.035 r_dihedral_angle_3_deg 12.573 r_dihedral_angle_1_deg 5.463 r_scangle_it 3.333 r_scbond_it 2.144 r_mcangle_it 1.975 r_angle_refined_deg 1.377 r_mcbond_it 1.174 r_angle_other_deg 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.532 r_dihedral_angle_4_deg 16.035 r_dihedral_angle_3_deg 12.573 r_dihedral_angle_1_deg 5.463 r_scangle_it 3.333 r_scbond_it 2.144 r_mcangle_it 1.975 r_angle_refined_deg 1.377 r_mcbond_it 1.174 r_angle_other_deg 0.84 r_mcbond_other 0.306 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1482 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 8
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling