X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelOtherab initio

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5298Sodium Phosphate, Potassium Phosphate, pH 7.5, vapor diffusion, sitting drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6353.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.786α = 90
b = 68.386β = 132.67
c = 68.969γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDMARMOSAIC 300 mm CCD2007-12-09SINGLE WAVELENGTH
21x-ray298CCDMARMOSAIC 300 mm CCD2007-12-09SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.9APS22-ID
2SYNCHROTRONAPS BEAMLINE 22-ID1.9APS22-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
1,225092.70.04822.520216
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)
1,222.0786.70.10419.5

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 DIFFRACTIONSADTHROUGHOUTab initio219.341906410391000.175760.172910.22789RANDOM19.723
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]
-0.02-0.010.02-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.098
r_dihedral_angle_4_deg24.201
r_dihedral_angle_3_deg14.869
r_dihedral_angle_1_deg14.335
r_scangle_it5.145
r_scbond_it3.198
r_mcangle_it2.032
r_angle_refined_deg1.864
r_mcbond_it1.373
r_angle_other_deg1.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.098
r_dihedral_angle_4_deg24.201
r_dihedral_angle_3_deg14.869
r_dihedral_angle_1_deg14.335
r_scangle_it5.145
r_scbond_it3.198
r_mcangle_it2.032
r_angle_refined_deg1.864
r_mcbond_it1.373
r_angle_other_deg1.154
r_symmetry_vdw_refined0.292
r_mcbond_other0.287
r_symmetry_vdw_other0.259
r_chiral_restr0.24
r_nbd_refined0.221
r_nbd_other0.199
r_xyhbond_nbd_refined0.198
r_nbtor_refined0.163
r_xyhbond_nbd_other0.149
r_nbtor_other0.089
r_symmetry_hbond_refined0.078
r_bond_refined_d0.019
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2134
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms11

Software

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