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Crystal structure of alpha-amylase inhibitor wrightide R1 (wR1) peptide from Wrightia religiosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CLV PDB ENTRY 1CLV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 2 pH 2
Crystal Properties Matthews coefficient Solvent content 1.73 28.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 16.194 α = 90 b = 29.133 β = 90 c = 47.701 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 93 CCD MARRESEARCH 2013-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.25 25 95.4 0.03 23.2 3.3 6362 66
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 1.25 1.32 90.3 0.07 11.9 3.3
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 1CLV 1.25 24.86 6017 317 100 0.15787 0.15779 0.1582 0.15927 0.161 RANDOM 9.685
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] -0.13 0.42 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.768 r_dihedral_angle_3_deg 16.26 r_dihedral_angle_1_deg 3.735 r_scangle_it 1.484 r_angle_refined_deg 0.971 r_scbond_it 0.94 r_sphericity_free 0.75 r_sphericity_bonded 0.686 r_mcangle_it 0.588 r_rigid_bond_restr 0.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.768 r_dihedral_angle_3_deg 16.26 r_dihedral_angle_1_deg 3.735 r_scangle_it 1.484 r_angle_refined_deg 0.971 r_scbond_it 0.94 r_sphericity_free 0.75 r_sphericity_bonded 0.686 r_mcangle_it 0.588 r_rigid_bond_restr 0.449 r_mcbond_it 0.273 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 223 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement