5HYM

3-Hydroxybenzoate 6-hydroxylase from Rhodococcus jostii in complex with phosphatidylinositol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BJZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529830% PEG 4000, 0.2 M lithium sulphate, 0.1 M Tris-HCl pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.3547.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.98α = 90
b = 106.98β = 90
c = 143.39γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9763ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.343.6499.70.160.1720.0610.9928.47.518766
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)
12.32.381000.5475.8

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 REPLACEMENTTHROUGHOUT4BJZ2.343.6417415133799.530.210.20590.2617RANDOM33.408
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]
-0.35-0.350.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.94
r_dihedral_angle_4_deg15.175
r_dihedral_angle_3_deg14.121
r_dihedral_angle_1_deg6.944
r_mcangle_it3.818
r_mcbond_it2.444
r_mcbond_other2.444
r_angle_refined_deg1.753
r_angle_other_deg1.025
r_chiral_restr0.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.94
r_dihedral_angle_4_deg15.175
r_dihedral_angle_3_deg14.121
r_dihedral_angle_1_deg6.944
r_mcangle_it3.818
r_mcbond_it2.444
r_mcbond_other2.444
r_angle_refined_deg1.753
r_angle_other_deg1.025
r_chiral_restr0.097
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.006
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3078
Nucleic Acid Atoms
Solvent Atoms14
Heterogen Atoms106

Software

Software
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction