2V9P | pdb_00002v9p

Crystal structure of papillomavirus E1 hexameric helicase DNA-free form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GXAPDB ENTRY 2GXA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5K-PHOSPHATE PH 7.5, NACL, PEG3350, MES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.855

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.111α = 90
b = 180.649β = 90
c = 187.533γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
1325940.1113.54.88608867
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)
133.11730.512.43.5

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 2GXA324.958518985393.40.2190.2190.220.2710.27RANDOM77.51
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]
6.93-4.97-1.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.948
r_dihedral_angle_3_deg19.969
r_dihedral_angle_4_deg17.986
r_dihedral_angle_1_deg5.598
r_scangle_it2.731
r_scbond_it1.559
r_angle_refined_deg1.185
r_mcangle_it1.01
r_mcbond_it0.512
r_nbtor_refined0.314
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25948
Nucleic Acid Atoms
Solvent Atoms35
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing