2J4H

Crystal structure of a H121A Escherichia coli dCTP deaminase mutant enzyme


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.8VAPOUR DIFFUSION, 34% PEG400, 0.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH6.8, 5MM DCTP
Crystal Properties
Matthews coefficientSolvent content
2.5551.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.545α = 90
b = 62.545β = 90
c = 342.444γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-2MAX III911-2

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
12.75094.20.124.91011131
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)
12.72.8575.10.471.35.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONOTHERTHROUGHOUT2.7301053956393.40.2280.2250.273RANDOM29.14
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]
2.281.142.28-3.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.765
r_dihedral_angle_4_deg22.129
r_dihedral_angle_3_deg16.542
r_dihedral_angle_1_deg6.884
r_scangle_it2.093
r_angle_refined_deg1.579
r_scbond_it1.303
r_mcangle_it1.061
r_mcbond_it0.956
r_angle_other_deg0.911
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.765
r_dihedral_angle_4_deg22.129
r_dihedral_angle_3_deg16.542
r_dihedral_angle_1_deg6.884
r_scangle_it2.093
r_angle_refined_deg1.579
r_scbond_it1.303
r_mcangle_it1.061
r_mcbond_it0.956
r_angle_other_deg0.911
r_symmetry_hbond_refined0.24
r_symmetry_vdw_other0.224
r_nbd_refined0.211
r_nbd_other0.199
r_symmetry_vdw_refined0.151
r_chiral_restr0.089
r_nbtor_other0.087
r_xyhbond_nbd_refined0.07
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2656
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling