X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P5F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529830% PEG 3000, 100 mM HEPES, 200 mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0259.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.987α = 90
b = 74.987β = 90
c = 75.11γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATERIGAKU RAXIS IV++2007-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.542

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
11.5501000.04846.110.33955439554
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)
1.51.551000.2618.49.83866

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 REPLACEMENTTHROUGHOUT1P5F1.5503753137531198099.930.183070.183070.182020.20312RANDOM17.528
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]
0.460.230.46-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.956
r_dihedral_angle_4_deg19.161
r_dihedral_angle_3_deg10.445
r_dihedral_angle_1_deg5.55
r_scangle_it2.958
r_scbond_it1.771
r_angle_refined_deg1.205
r_mcangle_it1.056
r_mcbond_it0.674
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.956
r_dihedral_angle_4_deg19.161
r_dihedral_angle_3_deg10.445
r_dihedral_angle_1_deg5.55
r_scangle_it2.958
r_scbond_it1.771
r_angle_refined_deg1.205
r_mcangle_it1.056
r_mcbond_it0.674
r_nbtor_refined0.303
r_symmetry_vdw_refined0.214
r_symmetry_hbond_refined0.2
r_nbd_refined0.196
r_xyhbond_nbd_refined0.094
r_chiral_restr0.075
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1409
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing