8HL7

Crystal structure of p97 N/D1 in complex with a valosin-containing protein methyltransferase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LG1 
experimental modelPDB 1S3S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529520 % (w/v) polyethylene glycol (PEG) 3350, 0.1M Na-HEPES (pH 7.5), 2 % (v/v) Tacsimate (pH 7.0), and 3 % (w/v) 6-aminohexanoic acid
Crystal Properties
Matthews coefficientSolvent content
3.1661.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.78α = 90
b = 60.78β = 90
c = 473.91γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-09-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)1.0000PAL/PLS5C (4A)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.83099.80.0580.9748.812.72610360.32
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.950.310.89

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.829.571.3823284112199.70.21940.21720.260966.14
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.601
f_angle_d1.34
f_chiral_restr0.066
f_plane_restr0.0102
f_bond_d0.0094
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4574
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms96

Software

Software
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
HKL-2000data scaling
PHASERphasing