X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3I3KPDB ENTRY 3I3K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52912.5M (NH4)2SO4, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.8256.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.626α = 90
b = 146.626β = 90
c = 110.56γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-05-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97934CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.92599.30.1090.14738.311.526591-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.9395.40.5980.4943.55.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3I3K2.924.5226056137399.210.206360.202960.27206RANDOM65.486
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]
0.450.45-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.965
r_dihedral_angle_4_deg22.135
r_dihedral_angle_3_deg20.23
r_dihedral_angle_1_deg5.673
r_scangle_it1.957
r_angle_refined_deg1.254
r_scbond_it1.13
r_mcangle_it0.879
r_mcbond_it0.45
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.965
r_dihedral_angle_4_deg22.135
r_dihedral_angle_3_deg20.23
r_dihedral_angle_1_deg5.673
r_scangle_it1.957
r_angle_refined_deg1.254
r_scbond_it1.13
r_mcangle_it0.879
r_mcbond_it0.45
r_nbtor_refined0.314
r_symmetry_hbond_refined0.265
r_nbd_refined0.223
r_symmetry_vdw_refined0.223
r_xyhbond_nbd_refined0.164
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms7178
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms336

Software

Software
Software NamePurpose
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing