X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KHG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429812-30% PEG 3350, 0.1M HEPES pH 7.4, 10 mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1743.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.448α = 90
b = 119.046β = 109.59
c = 60.599γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Blue osmic confocal2007-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.54

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
11.85097.90.0813.17.3534695346922
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)
11.81.8693.20.5465.55077

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 REPLACEMENTTHROUGHOUT1KHG1.824.265345053450272197.830.180.180.1780.213RANDOM20.668
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]
0.230.05-0.15-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.124
r_dihedral_angle_4_deg18.504
r_dihedral_angle_3_deg13.585
r_dihedral_angle_1_deg5.466
r_scangle_it1.847
r_scbond_it1.106
r_angle_refined_deg1.079
r_mcangle_it0.731
r_mcbond_it0.395
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.124
r_dihedral_angle_4_deg18.504
r_dihedral_angle_3_deg13.585
r_dihedral_angle_1_deg5.466
r_scangle_it1.847
r_scbond_it1.106
r_angle_refined_deg1.079
r_mcangle_it0.731
r_mcbond_it0.395
r_nbtor_refined0.302
r_nbd_refined0.182
r_symmetry_vdw_refined0.179
r_symmetry_hbond_refined0.127
r_metal_ion_refined0.111
r_xyhbond_nbd_refined0.11
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4819
Nucleic Acid Atoms
Solvent Atoms579
Heterogen Atoms3

Software

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