4QPP

The Crystal Structure of Human HMT1 hnRNP methyltransferase-like protein 6 in complex with compound DS-421 (2-{4-[3-CHLORO-2-(2-METHOXYPHENYL)-1H-INDOL-5-YL]PIPERIDIN-1-YL}-N-METHYLETHANAMINE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HC4pdb entry 4HC4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62912.0 M NaForm, 0.1 M NaoAc, pH 4.6, vapor diffusion hanging drop, temperature 291K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.3547.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.884α = 90
b = 133.884β = 90
c = 133.419γ = 90
Symmetry
Space GroupP 42 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97856APS19-ID

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
12.52501000.1336.18.13368924180733.3
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)
12.522.561000.9048.22051

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 entry 4HC42.52504151983099.870.19150.19070.2345RANDOM37.597
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]
-0.25-0.250.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.876
r_dihedral_angle_4_deg14.805
r_dihedral_angle_3_deg13.154
r_dihedral_angle_1_deg5.28
r_mcangle_it2.248
r_mcbond_it1.295
r_mcbond_other1.294
r_angle_refined_deg1.117
r_angle_other_deg0.893
r_chiral_restr0.061
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.876
r_dihedral_angle_4_deg14.805
r_dihedral_angle_3_deg13.154
r_dihedral_angle_1_deg5.28
r_mcangle_it2.248
r_mcbond_it1.295
r_mcbond_other1.294
r_angle_refined_deg1.117
r_angle_other_deg0.893
r_chiral_restr0.061
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7685
Nucleic Acid Atoms
Solvent Atoms282
Heterogen Atoms155

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building