2UYC | pdb_00002uyc

HhaI DNA methyltransferase R163N mutant complex with 13mer GCGC-GMGC oligonucleotide and SAH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MHTPDB ENTRY 3MHT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.650 MM NA CITRATE PH 5.6, 1.8 M AMMONIUM SULFATE, 5% GLUCOSE
Crystal Properties
Matthews coefficientSolvent content
2.9558

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.99α = 90
b = 94.99β = 90
c = 312.903γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2006-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
1243.1599.80.0914.6536938213.6
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)
122.1199.70.334.65

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3MHT236.4136937372299.60.20.20.190.2270.22RANDOM19.5
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]
0.020.920.02-0.04
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.6
c_scangle_it1.57
c_angle_deg1.2
c_mcangle_it1.14
c_improper_angle_d1.04
c_scbond_it0.94
c_mcbond_it0.69
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.6
c_scangle_it1.57
c_angle_deg1.2
c_mcangle_it1.14
c_improper_angle_d1.04
c_scbond_it0.94
c_mcbond_it0.69
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2603
Nucleic Acid Atoms511
Solvent Atoms234
Heterogen Atoms86

Software

Software
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing