4BF4

PikC D50N mutant in complex with the engineered cycloalkane substrate mimic bearing a termianl N,N-dimethylamino group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BVJPDB ENTRY 2BVJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.527% PEG3350, 0.2 M LI SULFATE, 0.1 M NA CACODILATE, PH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.2244.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.273α = 66.48
b = 130.113β = 70.25
c = 134.898γ = 72.23
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCHMIRRORS2012-09-29MSINGLE 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
12.7119.8497.40.115.92.11696091.563.2
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)
12.72.8596.90.461.52.1

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 2BVJ2.7119.84161093847997.350.200090.19590.27903RANDOM45.865
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]
-0.390.71-0.680.01-0.530.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.744
r_dihedral_angle_4_deg19.318
r_dihedral_angle_3_deg17.829
r_dihedral_angle_1_deg6.171
r_scangle_it3.344
r_scbond_it2.025
r_mcangle_it1.771
r_angle_refined_deg1.464
r_rigid_bond_restr1.069
r_mcbond_it0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.744
r_dihedral_angle_4_deg19.318
r_dihedral_angle_3_deg17.829
r_dihedral_angle_1_deg6.171
r_scangle_it3.344
r_scbond_it2.025
r_mcangle_it1.771
r_angle_refined_deg1.464
r_rigid_bond_restr1.069
r_mcbond_it0.96
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.007
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms48831
Nucleic Acid Atoms
Solvent Atoms514
Heterogen Atoms790

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing