X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IF0PDB ENTRY 2IF0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5289Na Citrate, Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.0539.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.505α = 90
b = 77.777β = 90
c = 115.011γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2007-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

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
11.830.34595.70.0936.52.64534727.5
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)
11.81.8698.60.6341.252.54408

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2IF01.8304534741151220995.770.201450.199140.24474RANDOM17.074
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]
0.96-0.35-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.233
r_dihedral_angle_4_deg16.74
r_dihedral_angle_3_deg13.246
r_dihedral_angle_1_deg5.297
r_scangle_it1.78
r_scbond_it1.199
r_angle_refined_deg1.054
r_angle_other_deg0.825
r_mcangle_it0.75
r_mcbond_it0.676
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.233
r_dihedral_angle_4_deg16.74
r_dihedral_angle_3_deg13.246
r_dihedral_angle_1_deg5.297
r_scangle_it1.78
r_scbond_it1.199
r_angle_refined_deg1.054
r_angle_other_deg0.825
r_mcangle_it0.75
r_mcbond_it0.676
r_nbd_refined0.204
r_symmetry_vdw_other0.201
r_nbd_other0.182
r_nbtor_refined0.176
r_symmetry_hbond_refined0.152
r_xyhbond_nbd_refined0.143
r_mcbond_other0.104
r_symmetry_vdw_refined0.099
r_nbtor_other0.081
r_chiral_restr0.058
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
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 Atoms3773
Nucleic Acid Atoms
Solvent Atoms351
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing