3IS3

Crystal structure of 17beta-Hydroxysteroid dehydrogenase (Apo form) from fungus Cochliobolus lunatus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G0O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP827720% (W/V) PEG 6000, 20% (V/V) Glycerol, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6753.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.914α = 90
b = 67.914β = 90
c = 268.347γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platePlatinum Coated three segment toroidal mirror2005-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.2ELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.4828.899.60.0680.06819.213.55214052140-320.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.481.5198.40.4940.4944.16.41894

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 REPLACEMENTTHROUGHOUT1G0O1.4823.865184651846521598.360.176330.176330.174950.18828RANDOM24.853
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.394
r_dihedral_angle_3_deg11.113
r_dihedral_angle_4_deg9.426
r_dihedral_angle_1_deg6.041
r_scangle_it3.529
r_scbond_it2.227
r_angle_refined_deg1.422
r_mcangle_it1.304
r_mcbond_it0.773
r_chiral_restr0.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.394
r_dihedral_angle_3_deg11.113
r_dihedral_angle_4_deg9.426
r_dihedral_angle_1_deg6.041
r_scangle_it3.529
r_scbond_it2.227
r_angle_refined_deg1.422
r_mcangle_it1.304
r_mcbond_it0.773
r_chiral_restr0.104
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1964
Nucleic Acid Atoms
Solvent Atoms296
Heterogen Atoms15

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling