X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PIYPDB entry 1PIY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82982.0 M Sodium formate, 100 mM Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4249.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 192.04α = 90
b = 153.46β = 132
c = 143.36γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID0.97972APS17-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
12.53098.70.070.04814.73.6104627104627
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)
12.52.59880.7670.7671.22.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1PIY2.719.99706117061135521000.306920.30380.36797RANDOM41.924
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]
0.420.29-0.380.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.949
r_dihedral_angle_3_deg23.316
r_dihedral_angle_4_deg19.077
r_dihedral_angle_1_deg7.689
r_scangle_it3.103
r_scbond_it2.151
r_angle_refined_deg2.004
r_mcangle_it1.164
r_mcbond_it0.634
r_symmetry_vdw_refined0.508
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.949
r_dihedral_angle_3_deg23.316
r_dihedral_angle_4_deg19.077
r_dihedral_angle_1_deg7.689
r_scangle_it3.103
r_scbond_it2.151
r_angle_refined_deg2.004
r_mcangle_it1.164
r_mcbond_it0.634
r_symmetry_vdw_refined0.508
r_symmetry_hbond_refined0.451
r_nbtor_refined0.328
r_nbd_refined0.292
r_xyhbond_nbd_refined0.244
r_chiral_restr0.141
r_bond_refined_d0.022
r_gen_planes_refined0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16775
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms8

Software

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