X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KX3PDB ENTRY 1KX3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629185 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.9257.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.617α = 90
b = 109.856β = 90
c = 181.217γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98IMAGE PLATERIGAKU RAXIS IVosmic mirrors2006-09-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.542

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
12.6550.7910.0650.06520.96.36175156193
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)
2.652.7963.90.480.482.74.95579

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1KX32.65406193256123113690.620.2340.2340.2330.283RANDOM64.218
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]
1.87-1.09-0.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.509
r_dihedral_angle_4_deg22.437
r_dihedral_angle_3_deg17.427
r_dihedral_angle_1_deg5.086
r_scangle_it2.202
r_angle_refined_deg1.45
r_mcangle_it1.292
r_scbond_it1.234
r_mcbond_it0.727
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.509
r_dihedral_angle_4_deg22.437
r_dihedral_angle_3_deg17.427
r_dihedral_angle_1_deg5.086
r_scangle_it2.202
r_angle_refined_deg1.45
r_mcangle_it1.292
r_scbond_it1.234
r_mcbond_it0.727
r_nbtor_refined0.309
r_symmetry_hbond_refined0.234
r_symmetry_vdw_refined0.218
r_nbd_refined0.206
r_xyhbond_nbd_refined0.152
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6086
Nucleic Acid Atoms5939
Solvent Atoms122
Heterogen Atoms11

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction
CCP4data scaling
CNSphasing