X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2R7KPDB entry 2R7K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.229110% 2-propanol, 200 mM Li2SO4, 100 mM Na phosphate-citrate, pH 4.2, vapor diffusion, hanging drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.550.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.095α = 90
b = 127.222β = 102.85
c = 121.673γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702007-01-01MSINGLE WAVELENGTH
21IMAGE PLATERIGAKU RAXIS IV2007-05-05
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F10.91770CHESSF1
2ROTATING ANODERIGAKU1.54178

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
12.35098.80.1388.74.49898998928
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)
2.32.3898.50.2642.99860

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 REPLACEMENTTHROUGHOUTPDB entry 2R7K2.342.649898998928494198.670.2030.2030.2010.244RANDOM22.251
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]
0.37-1.66-1.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.627
r_dihedral_angle_3_deg14.87
r_dihedral_angle_4_deg9.23
r_dihedral_angle_1_deg5.711
r_scangle_it1.414
r_angle_refined_deg1.067
r_scbond_it0.827
r_mcangle_it0.735
r_mcbond_it0.419
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.627
r_dihedral_angle_3_deg14.87
r_dihedral_angle_4_deg9.23
r_dihedral_angle_1_deg5.711
r_scangle_it1.414
r_angle_refined_deg1.067
r_scbond_it0.827
r_mcangle_it0.735
r_mcbond_it0.419
r_nbtor_refined0.302
r_nbd_refined0.175
r_symmetry_vdw_refined0.153
r_xyhbond_nbd_refined0.117
r_symmetry_hbond_refined0.098
r_chiral_restr0.074
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16230
Nucleic Acid Atoms
Solvent Atoms541
Heterogen Atoms257

Software

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