6R77

Crystal structure of trans-3-Hydroxy-L-proline dehydratase in complex with substrate - closed conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W61 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Na HEPES 0.1 M, PEG 400, 2.0 Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.6954.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.415α = 90
b = 106.547β = 90
c = 149.456γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.9792ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
1286.895.70.07745.21.959449
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.10.29

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 REPLACEMENTTHROUGHOUT1W61245.0756179293595.720.189370.188180.21252RANDOM30.299
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]
4.49-0.69-3.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.284
r_dihedral_angle_4_deg15.475
r_dihedral_angle_3_deg14.172
r_dihedral_angle_1_deg7.508
r_long_range_B_refined6.71
r_long_range_B_other6.641
r_scangle_other5.014
r_scbond_it3.137
r_scbond_other3.136
r_mcangle_it2.909
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.284
r_dihedral_angle_4_deg15.475
r_dihedral_angle_3_deg14.172
r_dihedral_angle_1_deg7.508
r_long_range_B_refined6.71
r_long_range_B_other6.641
r_scangle_other5.014
r_scbond_it3.137
r_scbond_other3.136
r_mcangle_it2.909
r_mcangle_other2.909
r_mcbond_it1.993
r_mcbond_other1.992
r_angle_refined_deg1.44
r_angle_other_deg1.301
r_chiral_restr0.064
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5536
Nucleic Acid Atoms
Solvent Atoms397
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing