X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KM5PDB ENTRY 3KM5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52980.2M Calcium acetate, 30% PEG 8000, 0.1M Na cacodylate, pH 6.5, vapor diffusion, sitting drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.243.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.251α = 90
b = 123.131β = 91.25
c = 62.614γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2009-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.95663Australian SynchrotronMX1

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
11.565096.70.03219.12.48978215.1
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)
11.561.5973.20.1612.23401

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 3KM51.5623.2489740453597.290.1590.1580.191RANDOM18.413
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]
-0.24-0.31-1.141.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.922
r_dihedral_angle_4_deg12.599
r_dihedral_angle_3_deg9.273
r_dihedral_angle_1_deg7.281
r_scangle_it4.652
r_scbond_it3.327
r_mcangle_it2.758
r_mcbond_it1.923
r_angle_refined_deg1.551
r_angle_other_deg0.934
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.922
r_dihedral_angle_4_deg12.599
r_dihedral_angle_3_deg9.273
r_dihedral_angle_1_deg7.281
r_scangle_it4.652
r_scbond_it3.327
r_mcangle_it2.758
r_mcbond_it1.923
r_angle_refined_deg1.551
r_angle_other_deg0.934
r_mcbond_other0.651
r_chiral_restr0.092
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5240
Nucleic Acid Atoms
Solvent Atoms825
Heterogen Atoms17

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling