X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KPF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.629350% SATURATED AMMONIUM SULFATE SOLUTION, 0.1M SODIUM ACETATE PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.7474.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.676α = 90
b = 137.676β = 90
c = 189.148γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 42009-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.933BESSY14.1

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
13.246.51000.1958.653481334784-3
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)
3.23.311000.57835.1

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3KPF3.246.532998174999.930.193670.192470.21627RANDOM30.137
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]
1.550.771.55-2.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.696
r_dihedral_angle_3_deg17.128
r_dihedral_angle_4_deg13.418
r_dihedral_angle_1_deg5.006
r_scangle_it1.364
r_angle_refined_deg1.238
r_scbond_it0.796
r_mcangle_it0.617
r_mcbond_it0.321
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.696
r_dihedral_angle_3_deg17.128
r_dihedral_angle_4_deg13.418
r_dihedral_angle_1_deg5.006
r_scangle_it1.364
r_angle_refined_deg1.238
r_scbond_it0.796
r_mcangle_it0.617
r_mcbond_it0.321
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7487
Nucleic Acid Atoms
Solvent Atoms18
Heterogen Atoms174

Software

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