X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GWDPDB ENTRY 1GWD

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.346.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.889α = 90
b = 62.813β = 98.75
c = 87.099γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRFESRFID14-4

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
11.543.0596.30.0417.13.562347
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)
11.51.58950.373.23.5

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 1GWD1.543.0859169314896.280.138790.136730.17811RANDOM27.116
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]
0.88-0.331.23-1.97
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.097
r_dihedral_angle_2_deg32.595
r_sphericity_bonded17.84
r_dihedral_angle_4_deg13.102
r_dihedral_angle_3_deg12.949
r_rigid_bond_restr7.731
r_dihedral_angle_1_deg6.683
r_angle_refined_deg1.884
r_angle_other_deg1.539
r_chiral_restr0.177
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.097
r_dihedral_angle_2_deg32.595
r_sphericity_bonded17.84
r_dihedral_angle_4_deg13.102
r_dihedral_angle_3_deg12.949
r_rigid_bond_restr7.731
r_dihedral_angle_1_deg6.683
r_angle_refined_deg1.884
r_angle_other_deg1.539
r_chiral_restr0.177
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_gen_planes_other0.006
r_bond_other_d0.005
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3001
Nucleic Acid Atoms
Solvent Atoms358
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing