5FOI | pdb_00005foi

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CV9	PDB ENTRY 3CV9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		20% PEG 3350, 0.2 M CA ACETATE, 20 MM SPERMIDINE, 0.84 MM TCEP, pH 7

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.4

Crystal Data

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

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MARRESERCH	MIRRORS	2015-09-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.21	71	91.1	0.24	3.8	2		36326		0.5	31.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.21	2.33	71.2		1.47	1.3	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3CV9	2.21	71	34383	1838	90.81	0.18572	0.18227	0.19	0.2515	0.25	RANDOM	27.168

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	-1.47	0.37	1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.67
r_dihedral_angle_4_deg	18.16
r_dihedral_angle_3_deg	15.649
r_dihedral_angle_1_deg	6.595
r_long_range_B_refined	4.87
r_long_range_B_other	4.87
r_scangle_other	3.133
r_mcangle_it	2.886
r_mcangle_other	2.886
r_scbond_it	2.003
r_scbond_other	2.002
r_angle_refined_deg	1.907
r_mcbond_it	1.863
r_mcbond_other	1.862
r_angle_other_deg	1.35
r_chiral_restr	0.109
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001
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 Atoms	Number
Protein Atoms	6013
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	200

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MrBUMP	phasing