4IS3

Crystal structure of a 3alpha-hydroxysteroid dehydrogenase (BaiA2) associated with secondary bile acid synthesis from Clostridium scindens VPI12708 in complex with a putative NAD(+)-OH- adduct at 2.0 A resolution


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 293.0
Details 0.1M tris hydrochloride pH 8.5, 30% polyethylene glycol 4000, 0.2M sodium acetate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.51 α = 90
b = 92.89 β = 90.78
c = 82.92 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD double crystal monochromator 2010-05-14
Diffraction Radiation
Monochromator Protocol
double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162, 0.97936, 0.97919 SSRL BL9-2

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2 29.01 97.2 0.091 -- -- 3.8 -- 68376 -- -3.0 25.317
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.0 2.05 88.9 0.649 -- 2.3 3.6 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MAD 2.0 29.007 -- 0.0 -- 68331 3444 97.36 -- 0.1534 0.1519 0.182 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.0 2.05 -- 238 4569 0.2095 0.2384 -- 97.36
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.2578
Anisotropic B[1][1] 7.151
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -2.0607
Anisotropic B[2][2] -0.1745
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.9766
RMS Deviations
Key Refinement Restraint Deviation
t_other_torsion 2.73
t_angle_deg 1.0
t_bond_d 0.01
t_omega_torsion 3.09
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.216
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7440
Nucleic Acid Atoms 0
Heterogen Atoms 188
Solvent Atoms 751

Software

Software
Software Name Purpose
MOLPROBITY validation version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
XSCALE data processing version: January 30, 2009
BUSTER-TNT refinement version: 2.10.0
XDS data reduction
XSCALE data scaling
SHELXD phasing
BUSTER refinement version: 2.10.0