X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DNZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52930.1M Bis-tris, 1.45M (NH4)2SO4, 0.1M NaCl, 30%(w/v) 1,5-Diaminopentane dihydrochloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.766.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.534α = 90
b = 143.444β = 90
c = 172.82γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9796SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
125098.50.10.0716.661788661761831123.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0798.50.5950.5313.055.717439

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 REPLACEMENTTHROUGHOUT4DNZ230.44170200167273881898.280.172570.170750.20747RANDOM23.848
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]
-0.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.404
r_dihedral_angle_4_deg17.063
r_dihedral_angle_3_deg13.53
r_dihedral_angle_1_deg6.17
r_scangle_it5.322
r_scbond_it3.525
r_angle_refined_deg2.094
r_mcangle_it1.983
r_mcbond_it1.212
r_chiral_restr0.177
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.404
r_dihedral_angle_4_deg17.063
r_dihedral_angle_3_deg13.53
r_dihedral_angle_1_deg6.17
r_scangle_it5.322
r_scbond_it3.525
r_angle_refined_deg2.094
r_mcangle_it1.983
r_mcbond_it1.212
r_chiral_restr0.177
r_bond_refined_d0.028
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12084
Nucleic Acid Atoms
Solvent Atoms1317
Heterogen Atoms298

Software

Software
Software NamePurpose
HKL-2000data collection
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing