X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NPUPDB ENTRY 1NPU FOR CHAINS B,C, EARLY MODEL FOR CHAIN A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629820% PEG 3350, 200MM NH4H2PO4, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.652.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.46α = 90
b = 63.94β = 90
c = 159.92γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-32005-04-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BMAPS19-BM

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
12.655098.90.07512.3617320
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)
12.652.740.4343.8

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 1NPU FOR CHAINS B,C, EARLY MODEL FOR CHAIN A2.65201722589898.80.2140.2110.268RANDOM67.59
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]
1.96-1.41-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.473
r_dihedral_angle_4_deg17.544
r_dihedral_angle_3_deg17.421
r_dihedral_angle_1_deg6.569
r_scangle_it4.817
r_mcangle_it4.044
r_scbond_it2.842
r_mcbond_it2.322
r_angle_refined_deg1.4
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.473
r_dihedral_angle_4_deg17.544
r_dihedral_angle_3_deg17.421
r_dihedral_angle_1_deg6.569
r_scangle_it4.817
r_mcangle_it4.044
r_scbond_it2.842
r_mcbond_it2.322
r_angle_refined_deg1.4
r_nbtor_refined0.309
r_nbd_refined0.208
r_symmetry_hbond_refined0.207
r_symmetry_vdw_refined0.171
r_xyhbond_nbd_refined0.129
r_chiral_restr0.082
r_bond_refined_d0.014
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3562
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms6

Software

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