X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.450 MM SODIUM FORMATE, 16% PEG-3350, pH 7.4
Crystal Properties
Matthews coefficientSolvent content
2.1542.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.57α = 90
b = 50.56β = 97.15
c = 76.28γ = 90
Symmetry
Space GroupC 1 2 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
11.641.296.80.089.62.572363
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)
11.61.6998.40.51.82.5

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 1PPB1.637.168655364696.480.156160.154520.1873RANDOM16.614
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]
0.22-0.140.05-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.742
r_dihedral_angle_4_deg12.632
r_dihedral_angle_3_deg12.104
r_dihedral_angle_1_deg7.164
r_angle_refined_deg2.067
r_angle_other_deg1.411
r_chiral_restr0.128
r_bond_refined_d0.02
r_gen_planes_refined0.013
r_bond_other_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.742
r_dihedral_angle_4_deg12.632
r_dihedral_angle_3_deg12.104
r_dihedral_angle_1_deg7.164
r_angle_refined_deg2.067
r_angle_other_deg1.411
r_chiral_restr0.128
r_bond_refined_d0.02
r_gen_planes_refined0.013
r_bond_other_d0.008
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_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 Atoms4685
Nucleic Acid Atoms
Solvent Atoms473
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing