7OVG

The C146A variant of an amidase from Pyrococcus horikoshii with bound acetamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YPA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293The crystallization condition is: 5mg/mL protein, 0.1M potassium chloride, 0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.1M acetamide; Imidazole; MES monohydrate (acid); 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2244.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.979α = 68.09
b = 57.012β = 85.16
c = 61.358γ = 76.93
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray170PIXELDECTRIS EIGER2 XE 16M2019-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.6543.8681.140.0560.0650.0350.99611.323.45385222.57
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.70930.280.36710.44440.24630.9272.393

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 REPLACEMENTTHROUGHOUT6YPA1.6543.8551146266181.140.15270.151150.18204RANDOM29.106
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]
-0.020.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.411
r_dihedral_angle_4_deg16.634
r_dihedral_angle_3_deg12.49
r_long_range_B_other9.879
r_long_range_B_refined9.862
r_scangle_other9.208
r_scbond_it6.61
r_scbond_other6.608
r_dihedral_angle_1_deg6.506
r_mcangle_other4.142
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.411
r_dihedral_angle_4_deg16.634
r_dihedral_angle_3_deg12.49
r_long_range_B_other9.879
r_long_range_B_refined9.862
r_scangle_other9.208
r_scbond_it6.61
r_scbond_other6.608
r_dihedral_angle_1_deg6.506
r_mcangle_other4.142
r_mcangle_it4.13
r_mcbond_it3.222
r_mcbond_other3.207
r_angle_refined_deg1.626
r_angle_other_deg1.188
r_chiral_restr0.11
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4224
Nucleic Acid Atoms
Solvent Atoms207
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing