3O2V

Crystal structure of 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe, an engineered Diels-Alderase Fab with modified specificity and catalytic activity


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O5X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52931.75M ammoniumsulfate, 0.15M sodiumcitrate, 0.01% PEG20000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.5572.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.73α = 90
b = 128.73β = 90
c = 92.342γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002005-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.0ALS8.2.1

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
12.35099.40.05720.54.339314
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3899.70.5572.4

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 REPLACEMENTTHROUGHOUT2O5X2.35037304197399.40.193620.192250.2192RANDOM52.729
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]
2.031.012.03-3.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.741
r_dihedral_angle_4_deg18.831
r_dihedral_angle_3_deg15.367
r_dihedral_angle_1_deg7.086
r_scangle_it2.949
r_scbond_it2.251
r_angle_refined_deg1.816
r_mcangle_it1.359
r_mcbond_it1.055
r_angle_other_deg0.969
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.741
r_dihedral_angle_4_deg18.831
r_dihedral_angle_3_deg15.367
r_dihedral_angle_1_deg7.086
r_scangle_it2.949
r_scbond_it2.251
r_angle_refined_deg1.816
r_mcangle_it1.359
r_mcbond_it1.055
r_angle_other_deg0.969
r_symmetry_vdw_other0.271
r_symmetry_hbond_refined0.219
r_symmetry_vdw_refined0.217
r_nbd_other0.2
r_mcbond_other0.2
r_nbd_refined0.191
r_nbtor_refined0.182
r_xyhbond_nbd_refined0.177
r_chiral_restr0.103
r_nbtor_other0.087
r_xyhbond_nbd_other0.069
r_bond_refined_d0.019
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3344
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms184

Software

Software
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling