2BO1

Crystal structure of a hybrid ribosomal protein L30e with surface residues from T. celer, and core residues from yeast


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H7MPDB ENTRY 1H7M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.52UL 10MG/ML PROTEIN AND 2UL 22.5% PEG3350, 0.1M TRIS PH 8.5, CRYOPROTECTED IN 20% PEG 400
Crystal Properties
Matthews coefficientSolvent content
1.5821.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 29.187α = 90
b = 52.531β = 90
c = 52.692γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKERMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 6BPAL/PLS6B

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
11.72098.60.06635.6927763
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)
11.71.7694.90.09344.6

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 1H7M1.737.19879644598.50.1760.1730.24RANDOM8.22
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]
0.22-0.14-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.284
r_dihedral_angle_3_deg12.91
r_dihedral_angle_4_deg10.663
r_dihedral_angle_1_deg5.518
r_scangle_it3.465
r_scbond_it2.31
r_angle_refined_deg1.305
r_mcbond_it1.21
r_mcangle_it1.208
r_angle_other_deg0.776
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.284
r_dihedral_angle_3_deg12.91
r_dihedral_angle_4_deg10.663
r_dihedral_angle_1_deg5.518
r_scangle_it3.465
r_scbond_it2.31
r_angle_refined_deg1.305
r_mcbond_it1.21
r_mcangle_it1.208
r_angle_other_deg0.776
r_symmetry_vdw_other0.255
r_nbd_refined0.208
r_nbtor_refined0.175
r_nbd_other0.163
r_xyhbond_nbd_refined0.127
r_symmetry_vdw_refined0.12
r_symmetry_hbond_refined0.097
r_nbtor_other0.081
r_chiral_restr0.078
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_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 Atoms780
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling
CNSphasing