5UPD

Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate 1-Like protein 1 (WHSC1L1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OOIpdb entry 3OOI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529320% PEG-5000-MME, 0.1 M bis-tris, 0.02 M sarcosine
Crystal Properties
Matthews coefficientSolvent content
2.4148.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.16α = 90
b = 62.81β = 109.78
c = 48.84γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002015-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97957CLSI08ID-1

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
11.841.5598.90.1050.1240.0640.99511.13.723067
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)
11.81.8596.20.7140.8590.4710.6263.21678

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 3OOI1.841.5521949111898.790.18560.18390.218224.398
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]
1.350.47-0.52-0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.055
r_dihedral_angle_4_deg21.717
r_dihedral_angle_3_deg13.356
r_dihedral_angle_1_deg6.008
r_mcangle_it3.416
r_mcbond_it2.221
r_mcbond_other2.221
r_angle_refined_deg1.801
r_angle_other_deg1.033
r_chiral_restr0.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.055
r_dihedral_angle_4_deg21.717
r_dihedral_angle_3_deg13.356
r_dihedral_angle_1_deg6.008
r_mcangle_it3.416
r_mcbond_it2.221
r_mcbond_other2.221
r_angle_refined_deg1.801
r_angle_other_deg1.033
r_chiral_restr0.109
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1644
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
XDSdata reduction
PHASERphasing