X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PU4PDB ENTRY 1PU4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18pH 8.00
Crystal Properties
Matthews coefficientSolvent content
4.673

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 226.099α = 90
b = 226.099β = 90
c = 223.004γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.92093.30.1211910.469536
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)
12.9395.30.4746.410.4

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 1PU42.919.9669536347693.30.2420.2410.267RANDOM41.04
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]
-5.68-2.84-5.688.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.822
r_scangle_it2.705
r_angle_refined_deg1.891
r_scbond_it1.571
r_mcangle_it1.041
r_angle_other_deg0.99
r_mcbond_it0.539
r_symmetry_vdw_refined0.339
r_nbd_other0.234
r_symmetry_vdw_other0.228
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.822
r_scangle_it2.705
r_angle_refined_deg1.891
r_scbond_it1.571
r_mcangle_it1.041
r_angle_other_deg0.99
r_mcbond_it0.539
r_symmetry_vdw_refined0.339
r_nbd_other0.234
r_symmetry_vdw_other0.228
r_nbd_refined0.211
r_symmetry_hbond_refined0.188
r_xyhbond_nbd_refined0.177
r_chiral_restr0.1
r_nbtor_other0.094
r_bond_refined_d0.02
r_gen_planes_refined0.007
r_gen_planes_other0.005
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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_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 Atoms11063
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling