3B3R

Crystal structure of Streptomyces cholesterol oxidase H447Q/E361Q mutant bound to glycerol (0.98A)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MXTPDB ENTRY 1MXT; ADP, HETEROATOMS, WATERS AND ACTIVE SITE SIDECHAINS REMOVED FROM STARTING MODEL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.229110% PEG 8000, 75mM magnesium sulfate, 100mM cacodylate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.141.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.314α = 90
b = 73.643β = 104.98
c = 63.275γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315vertical focusing mirrorMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.93SSRLBL9-1

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
10.9838.1199.90.0667.83.752463152592846.9
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)
10.981.0299.90.482.13.38

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE RPDB ENTRY 1MXT; ADP, HETEROATOMS, WATERS AND ACTIVE SITE SIDECHAINS REMOVED FROM STARTING MODEL0.9834.42463151296994.90.12910.12920.1589RANDOM13.885
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
1273342.124503.74
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.094
s_non_zero_chiral_vol0.092
s_zero_chiral_vol0.082
s_similar_adp_cmpnt0.042
s_from_restr_planes0.033
s_angle_d0.029
s_bond_d0.012
s_rigid_bond_adp_cmpnt0.005
s_similar_dist
s_anti_bump_dis_restr
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3839
Nucleic Acid Atoms
Solvent Atoms754
Heterogen Atoms81

Software

Software
Software NamePurpose
d*TREKdata scaling
SHELXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
d*TREKdata reduction
REFMACphasing
SHELXL-97refinement