2ABA

Structure of reduced PETN reductase in complex with progesterone


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.229325%(w/v) PEG 3000, 0.1M trisodium citrate, 0.1M cacodylic acid(pH 6.2), 17%(v/v) isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.345.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.233α = 90
b = 68.636β = 90
c = 88.44γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9ESRFID14-1

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
111598.20.08711.14.2154638151855
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)
11.03840.4891.93.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1VYR1.0514.6154638151855801998.20.129460.129460.128390.15004RANDOM9.61
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]
0.540.07-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.142
r_dihedral_angle_4_deg16.23
r_dihedral_angle_3_deg12.179
r_dihedral_angle_1_deg5.913
r_sphericity_free4.204
r_scangle_it2.575
r_sphericity_bonded2.303
r_scbond_it1.847
r_angle_refined_deg1.497
r_mcangle_it1.414
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.142
r_dihedral_angle_4_deg16.23
r_dihedral_angle_3_deg12.179
r_dihedral_angle_1_deg5.913
r_sphericity_free4.204
r_scangle_it2.575
r_sphericity_bonded2.303
r_scbond_it1.847
r_angle_refined_deg1.497
r_mcangle_it1.414
r_rigid_bond_restr1.141
r_mcbond_it1.047
r_angle_other_deg0.854
r_mcbond_other0.419
r_symmetry_vdw_other0.292
r_nbd_other0.26
r_nbd_refined0.209
r_symmetry_hbond_refined0.19
r_xyhbond_nbd_refined0.143
r_chiral_restr0.088
r_nbtor_other0.086
r_symmetry_vdw_refined0.065
r_gen_planes_refined0.01
r_bond_refined_d0.009
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2840
Nucleic Acid Atoms
Solvent Atoms732
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing