3ZK5

PikC D50N mutant bound to the 10-DML analog with the 3-(N,N-dimethylamino)ethanoate anchoring group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4B7SPDB ENTRY 4B7S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
170.2 MGCL, 20% PEG 3350, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.141.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.419α = 90
b = 92.376β = 90.31
c = 69.251γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCHMIRRORS2013-01-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.8992.3889.80.116.73.6543111.521.6
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)
11.891.9984.10.641.53.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4B7S1.8969.2551511275389.170.200470.196950.26721RANDOM21.193
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]
0.48-0.23-1.130.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.354
r_dihedral_angle_4_deg20.496
r_dihedral_angle_3_deg14.866
r_dihedral_angle_1_deg6.385
r_scangle_it4.102
r_scbond_it2.85
r_angle_refined_deg1.928
r_mcangle_it1.638
r_mcbond_it1.028
r_chiral_restr0.135
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.354
r_dihedral_angle_4_deg20.496
r_dihedral_angle_3_deg14.866
r_dihedral_angle_1_deg6.385
r_scangle_it4.102
r_scbond_it2.85
r_angle_refined_deg1.928
r_mcangle_it1.638
r_mcbond_it1.028
r_chiral_restr0.135
r_bond_refined_d0.021
r_gen_planes_refined0.01
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_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 Atoms6119
Nucleic Acid Atoms
Solvent Atoms524
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing