X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K7MPDB CODE 3K7M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.529320mM Sodium phosphate; 4M sodium formiate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.968.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 164.162α = 90
b = 164.162β = 90
c = 164.162γ = 90
Symmetry
Space GroupP 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRROR2009-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW6MPG/DESY, HAMBURGBW6

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
12.65201000.156181922526256.3
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)
12.652.70.7463.7191108

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB CODE 3K7M2.6514.4212602116099.50.2020.1990.263RANDOM41.12
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.642
r_dihedral_angle_4_deg19.932
r_dihedral_angle_3_deg15.42
r_dihedral_angle_1_deg5.568
r_scangle_it2.568
r_scbond_it1.431
r_angle_refined_deg1.172
r_mcangle_it1.043
r_mcbond_it0.524
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.642
r_dihedral_angle_4_deg19.932
r_dihedral_angle_3_deg15.42
r_dihedral_angle_1_deg5.568
r_scangle_it2.568
r_scbond_it1.431
r_angle_refined_deg1.172
r_mcangle_it1.043
r_mcbond_it0.524
r_nbtor_refined0.312
r_symmetry_vdw_refined0.203
r_nbd_refined0.202
r_xyhbond_nbd_refined0.149
r_symmetry_hbond_refined0.127
r_chiral_restr0.077
r_bond_refined_d0.009
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3272
Nucleic Acid Atoms
Solvent Atoms284
Heterogen Atoms107

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling