X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4J38PDB ENTRY 4J38

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1 HEPES PH 7.5, 10% ISOPROPANOL, 20% PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.6554

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.16α = 90
b = 71.16β = 90
c = 75.42γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDRH-COATED TOROIDAL SI MIRROR2013-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-3MAX III911-3

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
13.1541.8586.30.126.32.256591.7
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)
13.153.3283.40.442.32.1

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 4J383.1535.61539326485.860.141740.13910.1956RANDOM43.137
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]
0.910.91-1.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.015
r_dihedral_angle_4_deg29.449
r_sphericity_bonded23.807
r_dihedral_angle_3_deg17.516
r_mcangle_it9.531
r_scbond_it7.807
r_mcbond_it7.267
r_mcbond_other7.226
r_dihedral_angle_1_deg7.073
r_rigid_bond_restr4.636
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.015
r_dihedral_angle_4_deg29.449
r_sphericity_bonded23.807
r_dihedral_angle_3_deg17.516
r_mcangle_it9.531
r_scbond_it7.807
r_mcbond_it7.267
r_mcbond_other7.226
r_dihedral_angle_1_deg7.073
r_rigid_bond_restr4.636
r_angle_refined_deg1.412
r_angle_other_deg0.726
r_chiral_restr0.073
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.002
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2104
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing