X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B4YPDB entry 2B4Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.530025% PEG 3350, 200mM NaCl, 0.1M Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.2845.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.2α = 90
b = 116.205β = 90.46
c = 55.993γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2005-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.00000

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.0658.1286.42809628096
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.062.186.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2B4Y2.0658.122666726667140286.20.2020.2020.1990.269RANDOM21.64
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]
0.2-0.170.2-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.413
r_dihedral_angle_4_deg19.211
r_dihedral_angle_3_deg15.905
r_dihedral_angle_1_deg5.297
r_angle_refined_deg1.73
r_scangle_it1.255
r_scbond_it0.818
r_mcangle_it0.562
r_mcbond_it0.331
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.413
r_dihedral_angle_4_deg19.211
r_dihedral_angle_3_deg15.905
r_dihedral_angle_1_deg5.297
r_angle_refined_deg1.73
r_scangle_it1.255
r_scbond_it0.818
r_mcangle_it0.562
r_mcbond_it0.331
r_nbtor_refined0.302
r_chiral_restr0.245
r_nbd_refined0.188
r_symmetry_vdw_refined0.159
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.127
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3947
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms88

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling