4RMG | pdb_00004rmg

Human Sirt2 in complex with SirReal2 and NAD+


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82770.1 M KSCN, 30% (wt/vol) PEG MME 2,000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.9157.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.701α = 90
b = 54.514β = 114.82
c = 96.693γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2013-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.8875.13100323351.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.92100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.8848.2830694164099.980.204540.202310.210.247330.26RANDOM37.891
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]
-1.18-0.951.650.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.347
r_dihedral_angle_4_deg16.589
r_dihedral_angle_3_deg14.347
r_dihedral_angle_1_deg6.4
r_long_range_B_refined6.341
r_long_range_B_other6.34
r_scangle_other4.177
r_mcangle_it3.369
r_mcangle_other3.368
r_scbond_it2.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.347
r_dihedral_angle_4_deg16.589
r_dihedral_angle_3_deg14.347
r_dihedral_angle_1_deg6.4
r_long_range_B_refined6.341
r_long_range_B_other6.34
r_scangle_other4.177
r_mcangle_it3.369
r_mcangle_other3.368
r_scbond_it2.69
r_scbond_other2.689
r_mcbond_it2.238
r_mcbond_other2.23
r_angle_refined_deg1.651
r_angle_other_deg0.87
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2350
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms74

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
Aimlessdata scaling