1MMI

E. COLI DNA POLYMERASE BETA SUBUNIT


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2POLPDB ENTRY 2POL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298100 mM Na/H MES, 50 to 60 mM CaCl2, 30% v/v PEG 400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.4249.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.012α = 90
b = 66.595β = 114.02
c = 80.779γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-12-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C1.00000APS14-BM-C

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
11.85500.0561.926204362043-2
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)
1.851.9291.70.4671.751.84

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2POL1.848506202658907311993.130.191190.188390.24461RANDOM26.719
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]
-0.880.371.67-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg20.324
r_scangle_it9.547
r_dihedral_angle_1_deg8.103
r_scbond_it6.38
r_mcangle_it3.975
r_mcbond_it2.545
r_angle_refined_deg1.37
r_angle_other_deg0.718
r_symmetry_hbond_other0.605
r_symmetry_vdw_other0.371
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg20.324
r_scangle_it9.547
r_dihedral_angle_1_deg8.103
r_scbond_it6.38
r_mcangle_it3.975
r_mcbond_it2.545
r_angle_refined_deg1.37
r_angle_other_deg0.718
r_symmetry_hbond_other0.605
r_symmetry_vdw_other0.371
r_xyhbond_nbd_other0.349
r_symmetry_hbond_refined0.344
r_symmetry_vdw_refined0.297
r_nbd_other0.293
r_nbd_refined0.26
r_xyhbond_nbd_refined0.253
r_chiral_restr0.109
r_nbtor_other0.094
r_gen_planes_refined0.022
r_gen_planes_other0.014
r_bond_refined_d0.008
r_bond_other_d0.003
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5865
Nucleic Acid Atoms
Solvent Atoms665
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement