1W4Z

Structure of actinorhodin polyketide (actIII) Reductase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EDOPDB ENTRY 1EDO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MOTHER LIQUOR 5 MG ML-1 PROTEIN AND 5 MM NADP IN 25 MM PHOSPHATE BUFFER PH 8 WITH 10%(V/V) GLYCEROL RESERVOIR SOLUTION 4.0-4.4 M SODIUM FORMATE
Crystal Properties
Matthews coefficientSolvent content
3.362.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.43α = 90
b = 103.43β = 90
c = 122.823γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.2SRSPX14.2

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
12.53099.80.07206.525371
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)
12.5301000.453.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1EDO2.53025371135299.80.1850.1830.218RANDOM45.91
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]
1.640.821.64-2.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.81
r_scangle_it6.495
r_scbond_it4.092
r_dihedral_angle_1_deg3.918
r_mcangle_it2.408
r_angle_refined_deg1.715
r_mcbond_it1.232
r_nbd_refined0.236
r_symmetry_vdw_refined0.231
r_symmetry_hbond_refined0.221
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.81
r_scangle_it6.495
r_scbond_it4.092
r_dihedral_angle_1_deg3.918
r_mcangle_it2.408
r_angle_refined_deg1.715
r_mcbond_it1.232
r_nbd_refined0.236
r_symmetry_vdw_refined0.231
r_symmetry_hbond_refined0.221
r_xyhbond_nbd_refined0.143
r_chiral_restr0.106
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3790
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms123

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing