X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FR2PDB ENTRY 1FR2, 1ZNV
experimental modelPDB 1ZNVPDB ENTRY 1FR2, 1ZNV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
110.529230% PEG40, pH10.5, Microbatch under oil, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.3748

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.65α = 90
b = 53.713β = 105.59
c = 79.334γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2007-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.155094.20.1540.1438.633.41598339.86
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5983.90.3270.2762.32.51405

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1FR2, 1ZNV2.4843.94165031516081491.860.244030.242330.27566RANDOM39.864
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]
-1.45-3.75-4.033.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.565
r_dihedral_angle_4_deg25.248
r_dihedral_angle_3_deg22.061
r_dihedral_angle_1_deg9.271
r_scangle_it5.236
r_scbond_it3.548
r_angle_refined_deg2.511
r_mcangle_it2.089
r_mcbond_it1.51
r_symmetry_vdw_refined0.359
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.565
r_dihedral_angle_4_deg25.248
r_dihedral_angle_3_deg22.061
r_dihedral_angle_1_deg9.271
r_scangle_it5.236
r_scbond_it3.548
r_angle_refined_deg2.511
r_mcangle_it2.089
r_mcbond_it1.51
r_symmetry_vdw_refined0.359
r_nbtor_refined0.325
r_nbd_refined0.282
r_xyhbond_nbd_refined0.219
r_chiral_restr0.177
r_symmetry_hbond_refined0.175
r_metal_ion_refined0.099
r_bond_refined_d0.028
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3226
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms2

Software

Software
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling