X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OPK1OPK: 154-235, 1FNF: loops omitted
experimental modelPDB 1FNF1OPK: 154-235, 1FNF: loops omitted

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529330% PEG 4000, 0.2M sodium acetate trihydrate, 0.1M Tris hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.244.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.625α = 90
b = 88.181β = 90
c = 131.081γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2008-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97872APS21-ID-D

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
11.7515095.30.0466.1384022
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.7511.81650.4381.92.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUT1OPK: 154-235, 1FNF: loops omitted1.753924029738402192295.30.1830.1820.180.221RANDOM27.667
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]
-0.76-0.180.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.396
r_dihedral_angle_4_deg19.742
r_dihedral_angle_3_deg11.706
r_dihedral_angle_1_deg5.955
r_scangle_it2.935
r_scbond_it2.27
r_angle_refined_deg1.5
r_mcangle_it1.482
r_mcbond_it0.934
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.396
r_dihedral_angle_4_deg19.742
r_dihedral_angle_3_deg11.706
r_dihedral_angle_1_deg5.955
r_scangle_it2.935
r_scbond_it2.27
r_angle_refined_deg1.5
r_mcangle_it1.482
r_mcbond_it0.934
r_nbtor_refined0.303
r_symmetry_vdw_refined0.232
r_nbd_refined0.201
r_symmetry_hbond_refined0.196
r_xyhbond_nbd_refined0.147
r_chiral_restr0.101
r_bond_refined_d0.017
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3089
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms10

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling