X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4QB1PDB ENTRY 4QB1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729320% PEG 6000, 0.2M Calcium chloride, 0.1M HEPES, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.856.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.891α = 90
b = 47.552β = 90
c = 102.735γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS 6M-F2014-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.978583PETRA III, EMBL c/o DESYP13 (MX1)

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
11.5102.7499.60.0970.0281612.941419232026119.94
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)
11.51.581000.510.1465.1134619

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTPDB ENTRY 4QB11.551.371141419230348161899.550.155690.154990.16882RANDOM14.625
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]
-0.070.86-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.124
r_dihedral_angle_4_deg18.933
r_dihedral_angle_3_deg12.155
r_dihedral_angle_1_deg7.24
r_long_range_B_refined4.436
r_long_range_B_other4.272
r_scangle_other3.198
r_scbond_it2.272
r_scbond_other2.247
r_mcangle_other2.185
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.124
r_dihedral_angle_4_deg18.933
r_dihedral_angle_3_deg12.155
r_dihedral_angle_1_deg7.24
r_long_range_B_refined4.436
r_long_range_B_other4.272
r_scangle_other3.198
r_scbond_it2.272
r_scbond_other2.247
r_mcangle_other2.185
r_mcangle_it2.179
r_angle_refined_deg1.84
r_mcbond_it1.372
r_mcbond_other1.356
r_angle_other_deg0.905
r_chiral_restr0.117
r_bond_refined_d0.022
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms981
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms28

Software

Software
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling