4UMZ

PikC D50N mutant in complex with the engineered substrate mimic bearing a 2-dimethylaminomethylbenzoate group


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.64% TACSIMATE, PH 5.5, 16% PEG3350, 0.1M NA CITRATE, PH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.6954.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.061α = 90
b = 110.703β = 90
c = 151.626γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCHMIRRORS2014-03-26MSINGLE 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
12.32151.6293.50.127.34.1409521.539.3
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)
12.322.4569.90.711.52.7

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 2VZM2.3262.6338801206993.130.19280.190040.24451RANDOM33.859
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]
0.44-0.29-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.932
r_dihedral_angle_4_deg20.099
r_dihedral_angle_3_deg15.355
r_dihedral_angle_1_deg6.093
r_mcangle_it4.046
r_scbond_it3.031
r_mcbond_it2.552
r_mcbond_other2.55
r_angle_refined_deg1.769
r_angle_other_deg0.878
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.932
r_dihedral_angle_4_deg20.099
r_dihedral_angle_3_deg15.355
r_dihedral_angle_1_deg6.093
r_mcangle_it4.046
r_scbond_it3.031
r_mcbond_it2.552
r_mcbond_other2.55
r_angle_refined_deg1.769
r_angle_other_deg0.878
r_chiral_restr0.1
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms6094
Nucleic Acid Atoms
Solvent Atoms449
Heterogen Atoms152

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing