7NB5

Structure of EstD11 S144A in complex with naproxen p-nitrophenol ester


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7AT0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5291Sodium formate 3.2M and citrate pH 5 0.1M
Crystal Properties
Matthews coefficientSolvent content
2.1141.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.999α = 90
b = 89.705β = 90
c = 125.762γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.1344.8499.90.0670.0270.99818.26.715581
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.132.191000.2310.090.9898.2

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 REPLACEMENTTHROUGHOUT7AT02.1342.361481276899.740.170270.167380.22773RANDOM39.253
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]
-2.334.43-2.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.465
r_dihedral_angle_4_deg19.041
r_long_range_B_other14.026
r_long_range_B_refined13.991
r_dihedral_angle_3_deg13.875
r_scangle_other13.177
r_scbond_it10.773
r_scbond_other10.769
r_mcangle_other7.515
r_mcangle_it7.492
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.465
r_dihedral_angle_4_deg19.041
r_long_range_B_other14.026
r_long_range_B_refined13.991
r_dihedral_angle_3_deg13.875
r_scangle_other13.177
r_scbond_it10.773
r_scbond_other10.769
r_mcangle_other7.515
r_mcangle_it7.492
r_mcbond_other6.265
r_mcbond_it6.263
r_dihedral_angle_1_deg5.2
r_angle_refined_deg1.237
r_angle_other_deg1.049
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2247
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing