4U6B

Zg3597, a family 117 glycoside hydrolase, produced by the marine bacterium Zobellia galactanivorans

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3P2N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	The optimized crystallization conditions for Zg3597 were: 16% glycerol, 0.15 M ammonium sulfate, and 20 % PEG 4000 in a 1:1 ratio with protein at 5 and 2.5 mg/mL and 14% PEG 3350 and 75 mM sodium acetate with a ratio of 2:1 protein (at 7.5 mg/mL) to mother liquor.

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.79	α = 90
b = 223.52	β = 90
c = 225.22	γ = 90

Symmetry
Space Group	F 2 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 315r		2012-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.979	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	30	99.7	13.2	6		103865

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42

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	3P2N	2.3	30	98705	5189	99.68	0.18016	0.1778	0.18	0.22521	0.22	RANDOM	38.537

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]
-1.66			1.24		0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.665
r_dihedral_angle_4_deg	19.325
r_dihedral_angle_3_deg	17.178
r_long_range_B_refined	9.322
r_dihedral_angle_1_deg	7.569
r_mcangle_it	5.806
r_scbond_it	4.539
r_mcbond_it	3.801
r_angle_refined_deg	1.885
r_chiral_restr	0.136
r_bond_refined_d	0.017
r_gen_planes_refined	0.011
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_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10693
Nucleic Acid Atoms
Solvent Atoms	701
Heterogen Atoms	67

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing