2Y98

Structure of the mixed-function P450 MycG in complex with mycinamicin IV in P21212 space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z36PDB ENTRY 2Z36

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.52968% PEG 4000, 0.2 M AMMONIUM SULFATE, 0.1 M BISTRIS PH 5.5, TEMP 23 C
Crystal Properties
Matthews coefficientSolvent content
2.4549.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.285α = 90
b = 162.025β = 90
c = 50.394γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCHMIRRORS2009-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.6581.0184.90.07156.4479441.522.8
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)
11.651.7440.60.631.63.3

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 2Z361.65162.0245438243284.720.150750.147850.20611RANDOM20.986
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]
-1.642.78-1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.591
r_dihedral_angle_4_deg19.251
r_dihedral_angle_3_deg14.232
r_scangle_it7.4
r_dihedral_angle_1_deg5.602
r_scbond_it5.288
r_mcangle_it3.13
r_rigid_bond_restr2.715
r_angle_refined_deg2.173
r_mcbond_it2.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.591
r_dihedral_angle_4_deg19.251
r_dihedral_angle_3_deg14.232
r_scangle_it7.4
r_dihedral_angle_1_deg5.602
r_scbond_it5.288
r_mcangle_it3.13
r_rigid_bond_restr2.715
r_angle_refined_deg2.173
r_mcbond_it2.094
r_chiral_restr0.151
r_bond_refined_d0.028
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3084
Nucleic Acid Atoms
Solvent Atoms397
Heterogen Atoms115

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing