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X-ray Crystal Structure of Chemically Synthesized Crambin-{alpha}carboxamide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 X-ray
crystallography-quality crystals for crambin-carboxamide were formed by mixing 2 ul of protein (10 mg/ml in pH 7.5 100mM HEPES buffer containing 150 mM NaCl) and 2 ul of a 0.8 M succinic acid (used for X-ray diffraction), or by mixing 2 ul of the protein solution with 2 ul of 0.1 M HEPES buffer containing 15% v/v tacsimate and 2% w/v polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.83 32.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.581 α = 90 b = 67.581 β = 90 c = 39.487 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B APS 5ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 20 4566 4354
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.601 1.643
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 20 4566 4354 212 97.73 0.2165 0.2165 0.21552 0.2252 0.23385 0.2388 RANDOM 31.739
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] 2.59 1.3 2.59 -3.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.985 r_dihedral_angle_4_deg 16.58 r_dihedral_angle_3_deg 15.862 r_dihedral_angle_1_deg 6.117 r_scangle_it 2.922 r_scbond_it 2.306 r_angle_refined_deg 1.547 r_mcangle_it 1.42 r_mcbond_it 1.101 r_angle_other_deg 0.964
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.985 r_dihedral_angle_4_deg 16.58 r_dihedral_angle_3_deg 15.862 r_dihedral_angle_1_deg 6.117 r_scangle_it 2.922 r_scbond_it 2.306 r_angle_refined_deg 1.547 r_mcangle_it 1.42 r_mcbond_it 1.101 r_angle_other_deg 0.964 r_symmetry_hbond_refined 0.327 r_nbd_refined 0.227 r_mcbond_other 0.216 r_nbd_other 0.198 r_symmetry_vdw_other 0.155 r_xyhbond_nbd_refined 0.146 r_symmetry_vdw_refined 0.137 r_nbtor_other 0.087 r_chiral_restr 0.072 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 299 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement