X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FRXpdb entry 3frx

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291Mix 0.5uL precipitant (6% PEG20000, 8% PEG-MME550, 0.2M calcium acetate), 0.5uL protein stock solution (11 mg/mL protein), 0.2 uL additive (5% w/v polyvinylpyrrolidine K15), vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.4349.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.544α = 114.34
b = 72.922β = 96.44
c = 81.514γ = 90.12
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97934APS19-ID

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
12.34097.80.1069.891.958481
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)
2.32.34960.8651.051.82898

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 REPLACEMENTTHROUGHOUT. Change of flag assignment was followed by slow-cool simulated annealing (from temperature = 5000.0, phenix).pdb entry 3frx2.3305824120001000.2450.2440.2766phenix.reflection_file_converter --use-lattice-symmetry-in-r-free-flag-generation29.377
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]
-2.228-0.256-0.235-0.9250.4913.505
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.43
r_dihedral_angle_3_deg13.38
r_dihedral_angle_4_deg13.022
r_dihedral_angle_1_deg6.18
r_scangle_it1.213
r_angle_refined_deg1.1
r_angle_other_deg0.812
r_scbond_it0.79
r_mcangle_it0.456
r_mcbond_it0.249
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.43
r_dihedral_angle_3_deg13.38
r_dihedral_angle_4_deg13.022
r_dihedral_angle_1_deg6.18
r_scangle_it1.213
r_angle_refined_deg1.1
r_angle_other_deg0.812
r_scbond_it0.79
r_mcangle_it0.456
r_mcbond_it0.249
r_chiral_restr0.066
r_mcbond_other0.066
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8828
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms35

Software

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