X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.12982.0 M (NH4)2SO4, 2% (w/v) PEG 400, 10 mM hepes/naoh, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298 KK
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.797α = 90
b = 85.039β = 106.18
c = 66.059γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayAREA DETECTORMARRESEARCHosmic confocal maxflux2001-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
129995.80.0517.645.392955229552
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.0796.10.472.732.732956

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 REPLACEMENTTHROUGHOUT1kxo263.2527943148295.660.195620.193140.24328RANDOM34.125
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]
-0.18-0.09-0.60.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.472
r_scangle_it3.858
r_mcangle_it3.459
r_angle_refined_deg2.671
r_scbond_it2.454
r_mcbond_it2.072
r_symmetry_vdw_refined0.273
r_symmetry_hbond_refined0.248
r_nbd_refined0.24
r_xyhbond_nbd_refined0.182
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.472
r_scangle_it3.858
r_mcangle_it3.459
r_angle_refined_deg2.671
r_scbond_it2.454
r_mcbond_it2.072
r_symmetry_vdw_refined0.273
r_symmetry_hbond_refined0.248
r_nbd_refined0.24
r_xyhbond_nbd_refined0.182
r_chiral_restr0.147
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2780
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms55

Software

Software
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement