3KD1

Closed binary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IH7PDB entry 1IH7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52985% PEG 20000, 0.1M sodium acetate pH 5, 0.1M magnesium acetate, 0.1M Tris-HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7254.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.485α = 90
b = 121.657β = 90
c = 131.538γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATEMAR scanner 300 mm plateSi(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geomet ry2009-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.03315APS23-ID-B

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
12.66501000.10617.77.63696336963
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.662.761002.247.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONisomorphous replacementTHROUGHOUTPDB entry 1IH72.66303329133291357099.960.21190.207960.24826RANDOM41.056
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]
-2.730.342.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.214
r_dihedral_angle_3_deg15.168
r_dihedral_angle_4_deg14.094
r_dihedral_angle_1_deg4.505
r_angle_refined_deg0.916
r_scangle_it0.75
r_scbond_it0.412
r_mcangle_it0.308
r_mcbond_it0.161
r_chiral_restr0.063
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.214
r_dihedral_angle_3_deg15.168
r_dihedral_angle_4_deg14.094
r_dihedral_angle_1_deg4.505
r_angle_refined_deg0.916
r_scangle_it0.75
r_scbond_it0.412
r_mcangle_it0.308
r_mcbond_it0.161
r_chiral_restr0.063
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7379
Nucleic Acid Atoms648
Solvent Atoms321
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing