X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VPEPDB ENTRY 2VPE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP292HANGING-DROP VAPOUR-DIFFUSION METHOD AT 19 CELSIUS. CRYSTALLIZATION CONDITIONS: 20% PEG-4000, 20% ISO-PROPANOL, 0.1 M NA CITRATE
Crystal Properties
Matthews coefficientSolvent content
2.8456.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.75α = 90
b = 105.75β = 90
c = 51.42γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-11-16MSINGLE 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
11.626.441000.1211.47.1370792
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)
11.61.691000.63.17

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 2VPE1.674.7437079195399.90.2020.2010.218RANDOM21.98
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]
0.650.65-1.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.323
r_dihedral_angle_4_deg14.252
r_dihedral_angle_3_deg11.379
r_dihedral_angle_1_deg5.357
r_scangle_it3.125
r_scbond_it2.04
r_mcangle_it1.406
r_angle_refined_deg1.21
r_mcbond_it0.822
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.323
r_dihedral_angle_4_deg14.252
r_dihedral_angle_3_deg11.379
r_dihedral_angle_1_deg5.357
r_scangle_it3.125
r_scbond_it2.04
r_mcangle_it1.406
r_angle_refined_deg1.21
r_mcbond_it0.822
r_nbtor_refined0.302
r_nbd_refined0.192
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.137
r_symmetry_hbond_refined0.119
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms1477
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing