X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YNPPDB ENTRY 1YNP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.352930.1M of bis-Tris-methane pH 6.35, 0.1 M sodium malonate and 16 % (w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2344.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.331α = 90
b = 119.036β = 90
c = 150.854γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-30.999MAX III911-3

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
12.7542.199.60.1039.53.64463444634
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)
12.752.997.70.6323.56293

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1YNP2.7541.874234642346225099.450.244210.244210.242630.27396RANDOM34.037
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]
-0.350.280.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.892
r_dihedral_angle_4_deg20.024
r_dihedral_angle_3_deg17.492
r_dihedral_angle_1_deg6.438
r_scangle_it2.627
r_scbond_it1.423
r_angle_refined_deg1.261
r_mcangle_it1.126
r_angle_other_deg0.935
r_mcbond_it0.577
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.892
r_dihedral_angle_4_deg20.024
r_dihedral_angle_3_deg17.492
r_dihedral_angle_1_deg6.438
r_scangle_it2.627
r_scbond_it1.423
r_angle_refined_deg1.261
r_mcangle_it1.126
r_angle_other_deg0.935
r_mcbond_it0.577
r_mcbond_other0.069
r_chiral_restr0.065
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.003
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11574
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms

Software

Software
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling