4B7S

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4B7DPDB ENTRY 4B7D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.52 M AMMONIUM SULFATE, 0.1 M BIS TRIS, PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.1342.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.246α = 90
b = 92.023β = 90.48
c = 69.525γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCHMIRRORS2012-07-28MSINGLE 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
11.8492.0294.40.098.33.9631601.523.5
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)
11.841.9469.40.61.53.1

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 4B7D1.8461.2459932318794.380.168870.165860.2242RANDOM22.611
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]
-0.26-0.3-1.031.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.612
r_dihedral_angle_4_deg19.641
r_dihedral_angle_3_deg14.383
r_dihedral_angle_1_deg5.748
r_scangle_it4.497
r_scbond_it3.038
r_angle_refined_deg1.847
r_mcangle_it1.77
r_mcbond_it1.068
r_chiral_restr0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.612
r_dihedral_angle_4_deg19.641
r_dihedral_angle_3_deg14.383
r_dihedral_angle_1_deg5.748
r_scangle_it4.497
r_scbond_it3.038
r_angle_refined_deg1.847
r_mcangle_it1.77
r_mcbond_it1.068
r_chiral_restr0.13
r_bond_refined_d0.022
r_gen_planes_refined0.011
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 Atoms6109
Nucleic Acid Atoms
Solvent Atoms727
Heterogen Atoms224

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing