3NZ1

Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62980.2 potassium sodium tartrate, 2M ammonium sulfate, 0.1 M sodium citrate/citric acid, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1342.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.72α = 90
b = 60.72β = 90
c = 120.18γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror2009-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-21.013SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.5652.58599.80.0668.843724637246
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.561.641000.5040.5041.245386

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.5652.583724637189185699.70.17420.17230.2104RANDOM13.5747
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]
0.580.290.58-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.176
r_dihedral_angle_4_deg18.823
r_dihedral_angle_3_deg13.295
r_dihedral_angle_1_deg6.135
r_scangle_it5.32
r_scbond_it3.38
r_angle_refined_deg2.397
r_mcangle_it2.113
r_mcbond_it1.354
r_chiral_restr0.198
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.176
r_dihedral_angle_4_deg18.823
r_dihedral_angle_3_deg13.295
r_dihedral_angle_1_deg6.135
r_scangle_it5.32
r_scbond_it3.38
r_angle_refined_deg2.397
r_mcangle_it2.113
r_mcbond_it1.354
r_chiral_restr0.198
r_bond_refined_d0.027
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2007
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms72

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction