X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V27PDB ENTRY 2V27

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
11.6 M NAK2PO4, 4% (V/V) PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.6753.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.32α = 90
b = 60.12β = 94.07
c = 124.04γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
12.52590.40.082.341892
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)
12.52.64940.392.22.3

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 2V272.51040034127290.40.264810.26360.30203RANDOM37.801
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]
-18.15-4.74-17.5235.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.694
r_dihedral_angle_3_deg21.129
r_dihedral_angle_4_deg18.639
r_dihedral_angle_1_deg7.675
r_angle_refined_deg2.083
r_angle_other_deg1.614
r_chiral_restr0.123
r_bond_refined_d0.018
r_gen_planes_refined0.012
r_bond_other_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.694
r_dihedral_angle_3_deg21.129
r_dihedral_angle_4_deg18.639
r_dihedral_angle_1_deg7.675
r_angle_refined_deg2.083
r_angle_other_deg1.614
r_chiral_restr0.123
r_bond_refined_d0.018
r_gen_planes_refined0.012
r_bond_other_d0.008
r_gen_planes_other0.007
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
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 Atoms7949
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing