5C2M | pdb_00005c2m

The de novo evolutionary emergence of a symmetrical protein is shaped by folding constraints


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TL2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH2920.1M NaF, 0.05 M Bis-Tris propane pH 7.5, 10% polyethylene glycol 3,350.
Crystal Properties
Matthews coefficientSolvent content
2.1442.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.693α = 90
b = 60.929β = 90
c = 88.351γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2009-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5417

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.95099.80.04229.66.11965624.1
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)
11.91.9397.40.3032.64.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1TL21.95018599100299.770.19290.190680.20.234850.25RANDOM20.718
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]
1-0.5-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30
r_dihedral_angle_4_deg19.608
r_dihedral_angle_3_deg14.51
r_dihedral_angle_1_deg11.044
r_sphericity_free9.711
r_scangle_it5.132
r_sphericity_bonded4.64
r_scbond_it3.727
r_mcangle_it2.567
r_rigid_bond_restr2.389
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30
r_dihedral_angle_4_deg19.608
r_dihedral_angle_3_deg14.51
r_dihedral_angle_1_deg11.044
r_sphericity_free9.711
r_scangle_it5.132
r_sphericity_bonded4.64
r_scbond_it3.727
r_mcangle_it2.567
r_rigid_bond_restr2.389
r_angle_refined_deg1.902
r_mcbond_it1.637
r_chiral_restr0.158
r_bond_refined_d0.024
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other35.9
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 AtomsNumber
Protein Atoms1876
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing