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Structural and thermodynamic consequences of cyclization of peptide ligands for the recruitment site of cyclin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H28 PDB ENTRY 1H28
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 10MM HEPES PH 7, 100MM NACL 1.1 TO 1.25M AMMONIUM SULPHATE, 0.7 TO 0.85M KCL
Crystal Properties Matthews coefficient Solvent content 2.85 56.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.792 α = 90 b = 131.853 β = 90 c = 146.883 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R ELETTRA 5.2R
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 2.8 100 99.4 0.13 8.3 2 44032 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 2.8 2.95 92.5 0.57 1.6 2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1H28 2.8 100 33594 1764 99.41 0.21476 0.21093 0.28514 0.2491 RANDOM 47.203
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] -1.55 1.04 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.021 r_dihedral_angle_4_deg 18.931 r_dihedral_angle_3_deg 18.907 r_dihedral_angle_1_deg 6.964 r_scangle_it 1.95 r_angle_refined_deg 1.488 r_scbond_it 1.162 r_mcangle_it 1.039 r_mcbond_it 0.573 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.021 r_dihedral_angle_4_deg 18.931 r_dihedral_angle_3_deg 18.907 r_dihedral_angle_1_deg 6.964 r_scangle_it 1.95 r_angle_refined_deg 1.488 r_scbond_it 1.162 r_mcangle_it 1.039 r_mcbond_it 0.573 r_nbtor_refined 0.317 r_symmetry_hbond_refined 0.298 r_nbd_refined 0.241 r_symmetry_vdw_refined 0.213 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.114 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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_mcangle_other r_scbond_other 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 8732 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing