X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PV1PDB ENTRY 1PV1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6289200mm ammonium acetate, 30% PEG4000, pH5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
1.7830.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.542α = 90
b = 70.724β = 108.84
c = 65.014γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray193CCDADSC QUANTUM 315mirrors2008-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.55098.10.3250.32520.53.670703692892215.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.599.60.3250.32520.53.669289

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1PV11.540.1622692896576735001000.17860.176850.175810.19612RANDOM17.953
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]
-0.58-0.260.73-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.342
r_dihedral_angle_4_deg12.432
r_dihedral_angle_3_deg11.193
r_dihedral_angle_1_deg5.489
r_scangle_it2.93
r_scbond_it2.417
r_sphericity_bonded2.36
r_rigid_bond_restr2.325
r_sphericity_free1.431
r_mcangle_it1.253
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.342
r_dihedral_angle_4_deg12.432
r_dihedral_angle_3_deg11.193
r_dihedral_angle_1_deg5.489
r_scangle_it2.93
r_scbond_it2.417
r_sphericity_bonded2.36
r_rigid_bond_restr2.325
r_sphericity_free1.431
r_mcangle_it1.253
r_angle_refined_deg1.032
r_mcbond_it0.655
r_chiral_restr0.077
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
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_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4293
Nucleic Acid Atoms
Solvent Atoms603
Heterogen Atoms4

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling