4QPN

Crystal Structure of Human Methyltransferase-Like Protein 21B


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LECsolved with data from isomorphous crystal. model based on pdb entry 4LEC.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29320% PEG-3350, 0.2 M tri-lithium citrate. Protein sample was incubated with SAH overnight. Endopeptidase was added to the protein sample immediately prior to crystallization set up, vapor diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.6726.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.665α = 90
b = 38.665β = 90
c = 193.915γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDadsc q3152014-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97915APS19-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
11.2538.781000.09219.611.145170
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)
11.251.271000.956310.82181

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 REPLACEMENTTHROUGHOUTsolved with data from isomorphous crystal. model based on pdb entry 4LEC.1.2533.4845060219099.950.12380.12160.1667RANDOM12.1595
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]
0.030.010.03-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.43
r_sphericity_free19.118
r_dihedral_angle_4_deg18.485
r_dihedral_angle_3_deg12.301
r_sphericity_bonded8.001
r_dihedral_angle_1_deg6.948
r_rigid_bond_restr4.623
r_mcangle_it1.99
r_angle_refined_deg1.98
r_mcbond_other1.568
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.43
r_sphericity_free19.118
r_dihedral_angle_4_deg18.485
r_dihedral_angle_3_deg12.301
r_sphericity_bonded8.001
r_dihedral_angle_1_deg6.948
r_rigid_bond_restr4.623
r_mcangle_it1.99
r_angle_refined_deg1.98
r_mcbond_other1.568
r_mcbond_it1.567
r_angle_other_deg0.899
r_chiral_restr0.128
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1579
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms50

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction