X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DKVPDB entry 3DKV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829329% PEG MME 2000, 100mM NaCl, 100mM HEPPS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1141.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.003α = 90
b = 76.688β = 95.3
c = 77.993γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2007-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97934APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.535098.959416
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.531.58

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 3DKV1.5838.8454455275899.760.2020.20.239RANDOM18.394
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]
-0.03-0.06-0.320.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.705
r_dihedral_angle_4_deg17.787
r_dihedral_angle_3_deg13.704
r_dihedral_angle_1_deg5.318
r_scangle_it3.201
r_scbond_it2.064
r_angle_refined_deg1.508
r_mcangle_it1.293
r_mcbond_it0.833
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.705
r_dihedral_angle_4_deg17.787
r_dihedral_angle_3_deg13.704
r_dihedral_angle_1_deg5.318
r_scangle_it3.201
r_scbond_it2.064
r_angle_refined_deg1.508
r_mcangle_it1.293
r_mcbond_it0.833
r_nbtor_refined0.309
r_symmetry_vdw_refined0.224
r_symmetry_hbond_refined0.22
r_nbd_refined0.207
r_xyhbond_nbd_refined0.144
r_chiral_restr0.083
r_metal_ion_refined0.019
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3356
Nucleic Acid Atoms
Solvent Atoms535
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing