X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KV3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.25298100 mM HEPES pH 7.25, 1.25M Amm. sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5451.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.671α = 90
b = 71.671β = 90
c = 309.01γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.9794SSRLBL11-1

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
125094.90.07211.86.35320953209
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)
122.0978.20.2962.384.55332

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 REPLACEMENTTHROUGHOUT1KV3225532095320934821000.2310.2280.266RANDOM39.305
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]
1.31.3-2.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.904
r_dihedral_angle_3_deg17.398
r_dihedral_angle_4_deg15.947
r_dihedral_angle_1_deg7.01
r_scangle_it2.34
r_scbond_it1.614
r_angle_refined_deg1.361
r_mcangle_it1.049
r_mcbond_it0.865
r_angle_other_deg0.862
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.904
r_dihedral_angle_3_deg17.398
r_dihedral_angle_4_deg15.947
r_dihedral_angle_1_deg7.01
r_scangle_it2.34
r_scbond_it1.614
r_angle_refined_deg1.361
r_mcangle_it1.049
r_mcbond_it0.865
r_angle_other_deg0.862
r_nbd_other0.202
r_nbd_refined0.199
r_xyhbond_nbd_refined0.194
r_nbtor_refined0.178
r_symmetry_hbond_refined0.164
r_mcbond_other0.156
r_symmetry_vdw_other0.137
r_symmetry_vdw_refined0.1
r_nbtor_other0.088
r_chiral_restr0.085
r_xyhbond_nbd_other0.019
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5232
Nucleic Acid Atoms
Solvent Atoms262
Heterogen Atoms25

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
PHASERphasing