5E2B

Crystal structure of NTMT1 in complex with N-terminally methylated PPKRIA peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27726% PEG3350, 16% tacsimate
Crystal Properties
Matthews coefficientSolvent content
3.0659.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.268α = 90
b = 107.268β = 90
c = 205.604γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002015-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.829.6599.20.130.1330.0280.99927.721.164736
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.84981.181.2080.2570.873.621.13713

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTisomorphous structure of NTMT1 in complex with different peptide1.9529.6549282201999.310.15370.15240.1875THIN SHELLS (SFTOOLS)18.6
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]
0.140.070.14-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.292
r_dihedral_angle_4_deg18.934
r_dihedral_angle_3_deg12.196
r_dihedral_angle_1_deg6.172
r_angle_refined_deg1.766
r_angle_other_deg1.339
r_mcangle_it0.913
r_mcbond_it0.539
r_mcbond_other0.533
r_chiral_restr0.114
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.292
r_dihedral_angle_4_deg18.934
r_dihedral_angle_3_deg12.196
r_dihedral_angle_1_deg6.172
r_angle_refined_deg1.766
r_angle_other_deg1.339
r_mcangle_it0.913
r_mcbond_it0.539
r_mcbond_other0.533
r_chiral_restr0.114
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3642
Nucleic Acid Atoms
Solvent Atoms385
Heterogen Atoms115

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction