X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4C7DPDB ENTRY 4C7D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1 M BIS-TRIS PH 6.5, 4 % (W/V) PEG 6000, 5 % DMSO
Crystal Properties
Matthews coefficientSolvent content
3.362

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.79α = 90
b = 129.24β = 90
c = 149.94γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1202011-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-1CLSI08ID-1

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
1248.9599.40.188.85.6956162
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)
122.198.60.533.25.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4C7D297.8990731480699.250.158480.156430.19712RANDOM12.448
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]
0.50.28-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.42
r_dihedral_angle_4_deg18.952
r_dihedral_angle_3_deg12.562
r_dihedral_angle_1_deg6.59
r_angle_refined_deg1.855
r_scbond_it1.462
r_mcangle_it1.419
r_mcbond_it0.904
r_chiral_restr0.137
r_bond_refined_d0.019
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.42
r_dihedral_angle_4_deg18.952
r_dihedral_angle_3_deg12.562
r_dihedral_angle_1_deg6.59
r_angle_refined_deg1.855
r_scbond_it1.462
r_mcangle_it1.419
r_mcbond_it0.904
r_chiral_restr0.137
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7655
Nucleic Acid Atoms
Solvent Atoms1147
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling