4AW3

Structure of the mixed-function P450 MycG F286V mutant in complex with mycinamicin V in P1 space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Y98PDB ENTRY 2Y98

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.51.6 M AMMONIUM SULFATE, 0.1 M MES PH6.5, 10% V/V 1,4-DIOXANE
Crystal Properties
Matthews coefficientSolvent content
2.5150.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.455α = 90.43
b = 56.107β = 97.22
c = 76.422γ = 102.11
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCHMIRRORS2012-02-27MSINGLE 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
12.0575.7796.60.174.12.1541081.523.9
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)
12.052.1695.70.541.72.2

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 2Y982.0575.7751252275296.420.169340.16590.2347RANDOM22.672
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]
0.38-1.15-0.080.06-0.72-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.543
r_dihedral_angle_4_deg18.272
r_dihedral_angle_3_deg16.56
r_dihedral_angle_1_deg6.152
r_scangle_it5.302
r_scbond_it3.42
r_angle_refined_deg2.028
r_mcangle_it1.968
r_mcbond_it1.109
r_chiral_restr0.136
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.543
r_dihedral_angle_4_deg18.272
r_dihedral_angle_3_deg16.56
r_dihedral_angle_1_deg6.152
r_scangle_it5.302
r_scbond_it3.42
r_angle_refined_deg2.028
r_mcangle_it1.968
r_mcbond_it1.109
r_chiral_restr0.136
r_bond_refined_d0.022
r_gen_planes_refined0.01
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6124
Nucleic Acid Atoms
Solvent Atoms518
Heterogen Atoms250

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing