X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JPZPDB ENTRY 1JPZ CHAIN B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.83000.1 M sodium cacodylate, pH 5.8, 17% PEG3350, 0.14 M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.3447.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.158α = 90
b = 124.455β = 90
c = 127.691γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.344.90199.90.17611.85.31577415774
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)
13.33.481000.5140.5141.25.42260

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1JPZ CHAIN B3.344.9157151571583199.790.18330.18330.17880.2645RANDOM38.439
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]
-0.421.86-1.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.637
r_dihedral_angle_4_deg20.564
r_dihedral_angle_3_deg18.786
r_dihedral_angle_1_deg7.059
r_scangle_it2.855
r_angle_refined_deg1.652
r_scbond_it1.648
r_mcangle_it1.093
r_mcbond_it0.549
r_chiral_restr0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.637
r_dihedral_angle_4_deg20.564
r_dihedral_angle_3_deg18.786
r_dihedral_angle_1_deg7.059
r_scangle_it2.855
r_angle_refined_deg1.652
r_scbond_it1.648
r_mcangle_it1.093
r_mcbond_it0.549
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6890
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms86

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XSCALEdata scaling