2WMB

Structural and thermodynamic consequences of cyclization of peptide ligands for the recruitment site of cyclin A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.4BUFFER: 10MM HEPES PH 7.0, 100MM NACL. 1.1 TO 1.25M AMMONIUM SULPHATE, 0.7 TO 0.85MM KCL.
Crystal Properties
Matthews coefficientSolvent content
2.9658.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.747α = 90
b = 134.223β = 90
c = 148.236γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH SX-165MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2RELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.522.04950.0810.72460101.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.552.6989.30.521.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1H282.622.0441401221494.90.230.2260.296RANDOM45.71
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]
-0.340.180.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.419
r_dihedral_angle_4_deg19.899
r_dihedral_angle_3_deg18.329
r_dihedral_angle_1_deg7.391
r_scangle_it3.232
r_scbond_it2.073
r_angle_refined_deg1.702
r_mcangle_it1.529
r_mcbond_it0.876
r_symmetry_hbond_refined0.415
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.419
r_dihedral_angle_4_deg19.899
r_dihedral_angle_3_deg18.329
r_dihedral_angle_1_deg7.391
r_scangle_it3.232
r_scbond_it2.073
r_angle_refined_deg1.702
r_mcangle_it1.529
r_mcbond_it0.876
r_symmetry_hbond_refined0.415
r_nbtor_refined0.319
r_nbd_refined0.241
r_symmetry_vdw_refined0.241
r_xyhbond_nbd_refined0.162
r_chiral_restr0.116
r_bond_refined_d0.015
r_gen_planes_refined0.006
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 AtomsNumber
Protein Atoms8747
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing