X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K0MPDB ENTRY 1K0M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION829335%-50% PEG 400, 100mM Tris-HCl, pH8.0, 5mM GSH, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3146.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.015α = 90
b = 74.722β = 90
c = 79.827γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B0.9APS14-ID-B

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
11.8554.5593.90.0631.310.52314923144
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)
11.851.92620.32.84.9

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 1K0M1.8554.5520592111593.790.216650.214880.25038RANDOM33.893
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]
-2.710.22.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.644
r_dihedral_angle_4_deg15.777
r_dihedral_angle_3_deg15.027
r_dihedral_angle_1_deg6.195
r_scangle_it2.732
r_scbond_it1.942
r_angle_refined_deg1.538
r_angle_other_deg1.162
r_mcangle_it1.139
r_mcbond_it0.921
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.644
r_dihedral_angle_4_deg15.777
r_dihedral_angle_3_deg15.027
r_dihedral_angle_1_deg6.195
r_scangle_it2.732
r_scbond_it1.942
r_angle_refined_deg1.538
r_angle_other_deg1.162
r_mcangle_it1.139
r_mcbond_it0.921
r_symmetry_vdw_other0.294
r_symmetry_vdw_refined0.271
r_chiral_restr0.218
r_nbd_refined0.217
r_nbtor_refined0.188
r_symmetry_hbond_refined0.187
r_mcbond_other0.184
r_nbd_other0.176
r_xyhbond_nbd_refined0.154
r_nbtor_other0.086
r_xyhbond_nbd_other0.018
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1835
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing