X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62986% PEG 6000 and 0.1 M citric acid supplemented 0.2% of 3.0 M NTSB-195
Crystal Properties
Matthews coefficientSolvent content
2.4650

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.992α = 90
b = 65.992β = 90
c = 121.992γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1APS22-BM

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
12.4765.991000.1195.44.218742
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)
12.472.511000.483.7

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 REPLACEMENTTHROUGHOUT4HXD2.4765.991772298699.970.17670.17370.2257RANDOM24.713
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]
0.670.67-1.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.138
r_dihedral_angle_4_deg23.372
r_dihedral_angle_3_deg16.546
r_dihedral_angle_1_deg6.615
r_mcangle_it2.634
r_angle_refined_deg1.718
r_mcbond_it1.596
r_mcbond_other1.596
r_angle_other_deg0.873
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.138
r_dihedral_angle_4_deg23.372
r_dihedral_angle_3_deg16.546
r_dihedral_angle_1_deg6.615
r_mcangle_it2.634
r_angle_refined_deg1.718
r_mcbond_it1.596
r_mcbond_other1.596
r_angle_other_deg0.873
r_chiral_restr0.086
r_bond_refined_d0.014
r_bond_other_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3795
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms60

Software

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