2YCA

Mixed-function P450 MycG in complex with mycinamicin III in P21212 space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Y4HPDB ENTRY 2Y4H

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
170.6 M SUCCINIC ACID, PH 7.0 .
Crystal Properties
Matthews coefficientSolvent content
2.5852.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.747α = 90
b = 162.33β = 90
c = 49.789γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315rMIRRORS2011-03-02MSINGLE 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
11.881.1799.90.127.64.2435651.518.3
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)
11.81.999.90.931.54.3

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 2Y4H1.8162.3341348219199.740.15510.152160.21027RANDOM23.068
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]
0.260.57-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.716
r_dihedral_angle_4_deg19.86
r_dihedral_angle_3_deg14.896
r_scangle_it7.146
r_dihedral_angle_1_deg5.623
r_scbond_it4.88
r_mcangle_it2.908
r_rigid_bond_restr2.735
r_mcbond_it1.878
r_angle_refined_deg1.875
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.716
r_dihedral_angle_4_deg19.86
r_dihedral_angle_3_deg14.896
r_scangle_it7.146
r_dihedral_angle_1_deg5.623
r_scbond_it4.88
r_mcangle_it2.908
r_rigid_bond_restr2.735
r_mcbond_it1.878
r_angle_refined_deg1.875
r_chiral_restr0.122
r_bond_refined_d0.024
r_gen_planes_refined0.009
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 Atoms3090
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms117

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing