X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4OGXPDB ENTRY 4OGX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5FAB DX-2930 AT 268 UM OR 12.7 MG/ML AGAINST JCSG SCREEN CONDITION H3 AND ADDITIVE SCREEN 25% PEG-3350, 0.1 M BISTRIS PH 5.5, 0.1 M SODIUM CITRATE PH 4.5, 3% V/V DMSO, SUPPLEMENTED WITH 15% V/V ETHYLENE GLYCOL AS CRYO-PROTECTANT, PUCK ID TOZ7-6, CRYSTAL TRACKING ID 243341C6, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.93α = 90
b = 60.54β = 90
c = 150.49γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002013-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97982APS21-ID-F

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
11.755099.10.05122.4364334742967-326.55
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)
11.751.7999.80.4713.786.1

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 4OGX1.7539.2342901216799.130.1740.1720.214RANDOM22.06
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]
0.43-0.590.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.32
r_dihedral_angle_4_deg21.205
r_dihedral_angle_3_deg13.619
r_dihedral_angle_1_deg6.954
r_mcangle_it2.258
r_angle_refined_deg1.594
r_mcbond_it1.351
r_mcbond_other1.345
r_angle_other_deg0.822
r_chiral_restr0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.32
r_dihedral_angle_4_deg21.205
r_dihedral_angle_3_deg13.619
r_dihedral_angle_1_deg6.954
r_mcangle_it2.258
r_angle_refined_deg1.594
r_mcbond_it1.351
r_mcbond_other1.345
r_angle_other_deg0.822
r_chiral_restr0.1
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3154
Nucleic Acid Atoms
Solvent Atoms479
Heterogen Atoms1

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction