3KR9

Crystal structure of Streptococcus pneumoniae Sp1610, a putative tRNA (m1A22) methyltransferase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop2982.0M ammonium sulfate, 0.1M tri-sodium citrate pH5.6, 0.2M sodium/potassium tartrate, hanging drop, temperature 298K
Crystal Properties
Matthew coefficientSolvent content
358.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.807α = 90
b = 58.668β = 90
c = 142.995γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A0.97888, 0.97917, 0.96395Photon FactoryAR-NW12A

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
1271.4320787

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT271.4320787106498.230.2360.2340.289RANDOM28.211
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]
-1.78-1.323.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.732
r_dihedral_angle_3_deg16.68
r_dihedral_angle_4_deg15.611
r_dihedral_angle_1_deg6.075
r_scangle_it4.809
r_scbond_it3.081
r_angle_refined_deg1.695
r_mcangle_it1.67
r_mcbond_it0.973
r_chiral_restr0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.732
r_dihedral_angle_3_deg16.68
r_dihedral_angle_4_deg15.611
r_dihedral_angle_1_deg6.075
r_scangle_it4.809
r_scbond_it3.081
r_angle_refined_deg1.695
r_mcangle_it1.67
r_mcbond_it0.973
r_chiral_restr0.13
r_bond_refined_d0.02
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1735
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction