3CJR

Ribosomal protein L11 methyltransferase (PrmA) in complex with ribosomal protein L11 (K39A) and inhibitor Sinefungin.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1microbatch under oil8.5277170 mM sodium acetate trihydrate, 85 mM TRIS-HCl, 25.5 (w/v) PEG 4000, 15% (v/v) glycerol, 1 mM Sinefungin, pH 8.5, microbatch under oil, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7254.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.742α = 90
b = 132.742β = 90
c = 46.056γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Variable vertical and fixed horizontal slits. KOHZU double crystal monochromator with a water-cooled flat first crystal and a sagittally focused second crystal positioned for a fixed exit beam condition. Located ~18 m from source and ~6 m from sample position. Mirror system consisting of two vertically stacked, fused silica, spherical mirrors, to provide vertical focusing and harmonic rejection. One of the mirrors is rhodium coated and the other is uncoated. Located ~19.7 m from source.2007-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.9797NSLSX4A

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
12.055099.70.06718.73.727841-3
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)
12.052.12990.5282.33.45621

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 entries 2NXC, 2NXN2.052027841149199.960.216360.213220.27695RANDOM51.919
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]
-0.33-0.17-0.330.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.566
r_dihedral_angle_3_deg15.59
r_dihedral_angle_4_deg13.497
r_dihedral_angle_1_deg5.176
r_angle_refined_deg1.125
r_scangle_it0.971
r_scbond_it0.58
r_mcangle_it0.557
r_mcbond_it0.314
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.566
r_dihedral_angle_3_deg15.59
r_dihedral_angle_4_deg13.497
r_dihedral_angle_1_deg5.176
r_angle_refined_deg1.125
r_scangle_it0.971
r_scbond_it0.58
r_mcangle_it0.557
r_mcbond_it0.314
r_nbtor_refined0.297
r_nbd_refined0.177
r_symmetry_hbond_refined0.111
r_symmetry_vdw_refined0.103
r_xyhbond_nbd_refined0.093
r_chiral_restr0.067
r_bond_refined_d0.006
r_gen_planes_refined0.002
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 Atoms2791
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing