4L1X

Crystal Structuer of Human 3-alpha Hydroxysteroid Dehydrogenase Type 3 V54L Mutant in Complex with NADP+ and Progesterone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J96 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629525% PEG3350, 0.1M Sodium Cacodylate, 0.2M Ammonium Sulfate, 0.8mM Progesterone, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3146.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.14α = 90
b = 87.1β = 106.31
c = 76.87γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDRAYONIX MX225HE2012-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.979310APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
122598.7454764488522
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)
122.1196.60.0533.36376

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 REPLACEMENTTHROUGHOUT1J96224.642617226398.710.1420.139840.18255RANDOM11.131
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]
0.74-0.73-0.25-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.043
r_dihedral_angle_3_deg12.642
r_dihedral_angle_4_deg10.049
r_dihedral_angle_1_deg6.027
r_angle_refined_deg1.941
r_angle_other_deg1.286
r_chiral_restr0.114
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.043
r_dihedral_angle_3_deg12.642
r_dihedral_angle_4_deg10.049
r_dihedral_angle_1_deg6.027
r_angle_refined_deg1.941
r_angle_other_deg1.286
r_chiral_restr0.114
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.007
r_gen_planes_other0.006
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5206
Nucleic Acid Atoms
Solvent Atoms544
Heterogen Atoms152

Software

Software
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling