4L1W

Crystal Structuer of Human 3-alpha Hydroxysteroid Dehydrogenase Type 3 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
2.2846.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.8α = 90
b = 86.82β = 105.96
c = 76.49γ = 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)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
12.221.596.40.0373256122
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)
12.22.3295.90.0563.74701

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1J962.221.353256130919164096.410.148160.145730.19351RANDOM11.739
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]
0.39-0.98-0.350.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.476
r_dihedral_angle_3_deg13.123
r_dihedral_angle_4_deg12.506
r_dihedral_angle_1_deg5.832
r_angle_refined_deg1.902
r_angle_other_deg1.205
r_chiral_restr0.107
r_bond_refined_d0.017
r_gen_planes_refined0.011
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.476
r_dihedral_angle_3_deg13.123
r_dihedral_angle_4_deg12.506
r_dihedral_angle_1_deg5.832
r_angle_refined_deg1.902
r_angle_other_deg1.205
r_chiral_restr0.107
r_bond_refined_d0.017
r_gen_planes_refined0.011
r_bond_other_d0.006
r_gen_planes_other0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5204
Nucleic Acid Atoms
Solvent Atoms369
Heterogen Atoms152

Software

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