7RNP

Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9_H275E with 4-Cl-Trp non-covalently bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6AM8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.8529813-21% PEG3350 and 0.1 M Na HEPES pH 7.85
Crystal Properties
Matthews coefficientSolvent content
2.1843.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.162α = 90
b = 81.198β = 90
c = 321.014γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.03317APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.2540.00398.80.0460.9988.813.469911
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.30.8250.7031.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6AM82.2540.00369895348298.4480.2290.22730.266663.805
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]
-0.1613.811-3.649
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.963
r_dihedral_angle_3_deg13.142
r_dihedral_angle_4_deg12.377
r_dihedral_angle_1_deg6.592
r_lrange_it3.119
r_lrange_other3.116
r_chiral_restr_other1.795
r_scangle_it1.485
r_scangle_other1.485
r_mcangle_it1.432
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.963
r_dihedral_angle_3_deg13.142
r_dihedral_angle_4_deg12.377
r_dihedral_angle_1_deg6.592
r_lrange_it3.119
r_lrange_other3.116
r_chiral_restr_other1.795
r_scangle_it1.485
r_scangle_other1.485
r_mcangle_it1.432
r_mcangle_other1.432
r_angle_refined_deg1.202
r_angle_other_deg1.178
r_scbond_it0.901
r_scbond_other0.901
r_mcbond_other0.873
r_mcbond_it0.872
r_symmetry_xyhbond_nbd_refined0.275
r_nbd_other0.196
r_symmetry_nbd_other0.179
r_nbd_refined0.174
r_nbtor_refined0.152
r_xyhbond_nbd_refined0.144
r_symmetry_nbd_refined0.127
r_symmetry_nbtor_other0.075
r_chiral_restr0.042
r_gen_planes_refined0.005
r_bond_refined_d0.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11156
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing