4ASM

Crystal structure of the catalytic domain of beta-agarase D from Zobellia galactanivorans

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O4Z	PDB ENTRY 1O4Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		28-34 % PEG 8000 AND 0,1 M IMIDAZOLE PH 8, 4% ISOPROPANOL

Crystal Properties
Matthews coefficient	Solvent content
2.14	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.247	α = 90
b = 77.268	β = 90
c = 83.695	γ = 90

Symmetry
Space Group	P 21 21 21

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 210		2008-10-03	M	SINGLE WAVELENGTH

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

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	1.5	56	99.9	0.05	21.3	6.9		55977		0.1

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	1.5	1.58	99.9		0.25	9.1	6.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1O4Z	1.5	56.8	53071	2839	99.85	0.16354	0.16215	0.18987	RANDOM	13.7

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]
0.06			-0.03		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.495
r_dihedral_angle_4_deg	18.631
r_dihedral_angle_3_deg	12.873
r_dihedral_angle_1_deg	6.981
r_scangle_it	2.82
r_scbond_it	1.958
r_angle_refined_deg	1.441
r_mcangle_it	1.283
r_angle_other_deg	0.876
r_mcbond_it	0.784
r_nbd_other	0.324
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.232
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.2
r_symmetry_hbond_refined	0.179
r_chiral_restr	0.127
r_metal_ion_refined	0.075
r_nbtor_other	0.048
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms	Number
Protein Atoms	2843
Nucleic Acid Atoms
Solvent Atoms	595
Heterogen Atoms	13

Software

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