5FOI

Crystal structure of mycinamicin VIII C21 methyl hydroxylase MycCI from Micromonospora griseorubida bound to mycinamicin VIII


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1720% PEG 3350, 0.2 M CA ACETATE, 20 MM SPERMIDINE, 0.84 MM TCEP, pH 7
Crystal Properties
Matthews coefficientSolvent content
2.3447.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.781α = 83.2
b = 59.516β = 72.15
c = 74.623γ = 62.61
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESERCHMIRRORS2015-09-03MSINGLE 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
12.217191.10.243.82363260.531.6
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)
12.212.3371.21.471.31.9

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 3CV92.217134383183890.810.185720.182270.2515RANDOM27.168
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]
0.27-0.15-0.78-1.470.371.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.67
r_dihedral_angle_4_deg18.16
r_dihedral_angle_3_deg15.649
r_dihedral_angle_1_deg6.595
r_long_range_B_refined4.87
r_long_range_B_other4.87
r_scangle_other3.133
r_mcangle_it2.886
r_mcangle_other2.886
r_scbond_it2.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.67
r_dihedral_angle_4_deg18.16
r_dihedral_angle_3_deg15.649
r_dihedral_angle_1_deg6.595
r_long_range_B_refined4.87
r_long_range_B_other4.87
r_scangle_other3.133
r_mcangle_it2.886
r_mcangle_other2.886
r_scbond_it2.003
r_scbond_other2.002
r_angle_refined_deg1.907
r_mcbond_it1.863
r_mcbond_other1.862
r_angle_other_deg1.35
r_chiral_restr0.109
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6013
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms200

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MrBUMPphasing