X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KSGPDB ENTRY 1KSG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92770.1M bicine, 10% PEG 6000, 20mM hexammine cobalt (III) chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.9336.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.827α = 90
b = 44.081β = 111.46
c = 66.495γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 3152007-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.5596Photon FactoryBL-5A

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
12.255097.70.0650.06527.96.615074147271136.1
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)
2.252.3383.70.2160.21644.51496

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1KSG2.2535.9150741397574297.690.231680.231680.230110.26123RANDOM37.851
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]
-1.01-1.37-0.620.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.785
r_dihedral_angle_4_deg20.633
r_dihedral_angle_3_deg19.615
r_dihedral_angle_1_deg4.776
r_scangle_it2.799
r_mcangle_it1.919
r_scbond_it1.799
r_rigid_bond_restr1.379
r_angle_refined_deg1.327
r_mcbond_it1.043
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.785
r_dihedral_angle_4_deg20.633
r_dihedral_angle_3_deg19.615
r_dihedral_angle_1_deg4.776
r_scangle_it2.799
r_mcangle_it1.919
r_scbond_it1.799
r_rigid_bond_restr1.379
r_angle_refined_deg1.327
r_mcbond_it1.043
r_sphericity_bonded0.606
r_nbtor_refined0.314
r_nbd_refined0.23
r_symmetry_hbond_refined0.207
r_chiral_restr0.189
r_symmetry_vdw_refined0.161
r_xyhbond_nbd_refined0.136
r_sphericity_free0.096
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2483
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing