X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K4VPDB ENTRY 1K4V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
180.3M SODIUM CACODYLATE BUFFER, PH 6.5, 1.4M SODIUM ACETATE, 2% DIOXANE
Crystal Properties
Matthews coefficientSolvent content
4.4272

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.93α = 90
b = 103.26β = 90
c = 121.49γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2005-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.6SRSPX9.6

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
13.35099.80.27.611.718881
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)
13.33.4299.90.622.4596

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 1K4V3.2925.811770796099.10.2080.2050.28RANDOM36.12
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]
0.14-0.190.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.741
r_dihedral_angle_4_deg21.265
r_dihedral_angle_3_deg20.637
r_dihedral_angle_1_deg6.676
r_scangle_it2.352
r_angle_refined_deg1.544
r_mcangle_it1.419
r_scbond_it1.409
r_mcbond_it0.795
r_nbtor_refined0.335
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.741
r_dihedral_angle_4_deg21.265
r_dihedral_angle_3_deg20.637
r_dihedral_angle_1_deg6.676
r_scangle_it2.352
r_angle_refined_deg1.544
r_mcangle_it1.419
r_scbond_it1.409
r_mcbond_it0.795
r_nbtor_refined0.335
r_nbd_refined0.259
r_symmetry_vdw_refined0.227
r_xyhbond_nbd_refined0.161
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.005
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_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4612
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing