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_omega_torsion 3.09
t_angle_deg 1.0
t_bond_d 0.01
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

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
SHELXD,SHARP Structure Solution
BUSTER 2.10.0 Structure Refinement
Software
Software Name Purpose
BUSTER-TNT version: 2.10.0 refinement
Xscale version: January 30, 2009 data processing
SHARP phasing
SHELX phasing
pdb_extract version: 3.10 data extraction
MOLPROBITY version: 3beta29 validation