X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VL6SsoMCM N-terminal domain (2VL6), PfMCM ATPase domain (related entry 4R7Z)
experimental modelPDB 4R7ZSsoMCM N-terminal domain (2VL6), PfMCM ATPase domain (related entry 4R7Z)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.628110.8 mg/mL Sso-PfMCM; 5 mM ADP mixed 1:1 with 100 mM HEPES, pH 7.6; 350 mM MgCl2; 3 % (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
2.9357.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.902α = 90
b = 118.902β = 90
c = 199.317γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HS2014-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.75099.80.10714.86.84340743329-329.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.898.30.751.7954313

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 REPLACEMENTTHROUGHOUTSsoMCM N-terminal domain (2VL6), PfMCM ATPase domain (related entry 4R7Z)2.749.8339044197689.70.2630.2630.295RANDOM61.3
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]
-2.32-2.324.65
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.1
c_scangle_it2.75
c_mcangle_it2.6
c_scbond_it1.73
c_angle_deg1.5
c_mcbond_it1.46
c_improper_angle_d1.1
c_bond_d0.01
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.1
c_scangle_it2.75
c_mcangle_it2.6
c_scbond_it1.73
c_angle_deg1.5
c_mcbond_it1.46
c_improper_angle_d1.1
c_bond_d0.01
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 Atoms9430
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms64

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling