24TD | pdb_000024td

Crystal structure of GH30 Streptomyces avermitilis endo-beta-1,6-galactanase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.6 M ammonium sulfate, 0.1 M MES pH 6.5, 10% dioxane

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.128	α = 90
b = 50.128	β = 90
c = 331.431	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 315		2013-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	Photon Factory	BL-5A

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	100	100	0.144	17	13.8		35216

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	1.97			0.728	4.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.9	49.564	34947	1752	99.971	0.154	0.1524	0.166	0.1837	0.1919	RANDOM	21.973

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]
0.005			0.005		-0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.568
r_dihedral_angle_3_deg	10.707
r_dihedral_angle_1_deg	7.008
r_dihedral_angle_2_deg	5.664
r_lrange_it	4.534
r_lrange_other	4.408
r_scangle_it	2.905
r_scangle_other	2.905
r_scbond_it	2.043
r_scbond_other	2.043
r_mcangle_other	1.876
r_mcangle_it	1.875
r_mcbond_it	1.24
r_angle_refined_deg	1.236
r_mcbond_other	1.234
r_angle_other_deg	0.475
r_nbd_other	0.224
r_symmetry_nbd_refined	0.201
r_nbd_refined	0.199
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.168
r_xyhbond_nbd_refined	0.134
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.064
r_gen_planes_refined	0.006
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3547
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	133

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing