X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PPBPDB ENTRY 1PPB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.4100 MM SODIUM FORMATE, 18% PEG-3350, pH 7.4
Crystal Properties
Matthews coefficientSolvent content
2.1843.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.22α = 90
b = 51.33β = 96.13
c = 150.08γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2010-04-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.7543.4593.20.069.22.6105859
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)
11.751.8495.80.451.72.4

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 1PPB1.7542.14100531530592.90.211220.209550.24235RANDOM34.404
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]
-0.770.541.86-1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.485
r_dihedral_angle_3_deg14.74
r_dihedral_angle_4_deg13.263
r_dihedral_angle_1_deg6.978
r_angle_refined_deg1.802
r_angle_other_deg1.409
r_chiral_restr0.115
r_bond_refined_d0.017
r_gen_planes_refined0.012
r_bond_other_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.485
r_dihedral_angle_3_deg14.74
r_dihedral_angle_4_deg13.263
r_dihedral_angle_1_deg6.978
r_angle_refined_deg1.802
r_angle_other_deg1.409
r_chiral_restr0.115
r_bond_refined_d0.017
r_gen_planes_refined0.012
r_bond_other_d0.009
r_gen_planes_other0.008
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 Atoms8928
Nucleic Acid Atoms
Solvent Atoms424
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing