4IAG

Crystal structure of ZbmA, the zorbamycin binding protein from Streptomyces flavoviridis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	289	protein subject to reductive isopropylation, 0.8M Ammonium Sulfate, 0.1M Sodium Sitrate: HCl pH 4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.787	α = 90
b = 38.787	β = 90
c = 268.524	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210r		2012-08-03	M	SAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97929	APS	19-BM

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	1.9	50	98.5	0.068	11.2	9.7	10484	10484		-3	28.2

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	1.9	1.93	87.5		0.434		4	460

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.9	32.59	10243	10243	492	97.99	0.1913	0.1913	0.1893	0.2314	RANDOM	38.2635

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]
0.57	0.57		0.57		-1.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.801
r_dihedral_angle_4_deg	29.541
r_dihedral_angle_3_deg	13.403
r_dihedral_angle_1_deg	6.092
r_angle_refined_deg	1.836
r_angle_other_deg	1.398
r_chiral_restr	0.109
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.801
r_dihedral_angle_4_deg	29.541
r_dihedral_angle_3_deg	13.403
r_dihedral_angle_1_deg	6.092
r_angle_refined_deg	1.836
r_angle_other_deg	1.398
r_chiral_restr	0.109
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	946
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	38

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.