X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4IKP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529120% PEG 3350, 0.2 M AmSO4, 0.1 M Tris pH8.5
Crystal Properties
Matthews coefficientSolvent content
2.4950.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.091α = 90
b = 98.919β = 90
c = 207.553γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002016-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.885099.90.0890.0960.0346.27.7126636
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.911001.0210.757.36250

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 REPLACEMENTTHROUGHOUT4IKP1.8850123618252199.830.18840.18780.2152RANDOM28.661
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]
0.56-0.03-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.088
r_dihedral_angle_4_deg18.227
r_dihedral_angle_3_deg12.907
r_dihedral_angle_1_deg6.308
r_angle_refined_deg1.387
r_angle_other_deg0.916
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.088
r_dihedral_angle_4_deg18.227
r_dihedral_angle_3_deg12.907
r_dihedral_angle_1_deg6.308
r_angle_refined_deg1.387
r_angle_other_deg0.916
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10502
Nucleic Acid Atoms
Solvent Atoms700
Heterogen Atoms258

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction