2Y5Z

Mixed-function P450 MycG in complex with mycinamicin III in C2221 space group


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION729612.5% PEG MME 5000, 6% TACSIMATE, PH 7.0, 2% BENZAMIDINE HYDROCHLORIDE, 0.15 M NACL; TEMPERATURE 23 DEGREES CELSIUS.
Crystal Properties
Matthews coefficientSolvent content
2.448.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.305α = 90
b = 100.882β = 90
c = 439.37γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCHMIRRORS2010-11-20MSINGLE 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
12.06146.4686.30.089.84.4699121.530.4
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)
12.062.1742.30.361.51.4

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 2Y4H2.06219.6866285350186.330.153390.14980.22139RANDOM28.339
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]
0.080.31-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.734
r_dihedral_angle_4_deg20.262
r_dihedral_angle_3_deg15.077
r_scangle_it5.838
r_dihedral_angle_1_deg5.797
r_scbond_it3.816
r_mcangle_it2.251
r_rigid_bond_restr2.121
r_angle_refined_deg1.826
r_mcbond_it1.345
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.734
r_dihedral_angle_4_deg20.262
r_dihedral_angle_3_deg15.077
r_scangle_it5.838
r_dihedral_angle_1_deg5.797
r_scbond_it3.816
r_mcangle_it2.251
r_rigid_bond_restr2.121
r_angle_refined_deg1.826
r_mcbond_it1.345
r_chiral_restr0.114
r_bond_refined_d0.02
r_gen_planes_refined0.008
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 Atoms9253
Nucleic Acid Atoms
Solvent Atoms791
Heterogen Atoms327

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing