5JTS | pdb_00005jts

Structure of a beta-1,4-mannanase, SsGH134.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		alpha-helical fragment

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	The protein stock in the buffer of 20 mM sodium phosphate, pH7.2, and 200 mM NaCl is mixed 1:1 with the precipitant consist of 20 % PEG6000, 0.15-0.2 M CaCl2,and 0.1 M Na HEPES, pH7.0

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.91	α = 90
b = 53.68	β = 90
c = 81.45	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	PIXEL	DECTRIS PILATUS 6M		2016-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

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	1.09	33.62	99.9	0.066	12.2	6.1		68246		1.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.09	1.12	99.9		0.864	0.532	1.8	5.8

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	FREE R-VALUE	alpha-helical fragment	1.09	33.62	64732	3439	99.77	0.14039	0.13913	0.14	0.16316	0.13	RANDOM	14.314

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]
0.95			-0.48		-0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.306
r_sphericity_free	25.882
r_dihedral_angle_4_deg	20.366
r_dihedral_angle_3_deg	10.559
r_sphericity_bonded	9.236
r_dihedral_angle_1_deg	4.932
r_long_range_B_refined	3.018
r_long_range_B_other	3.017
r_rigid_bond_restr	2.073
r_scangle_other	1.996
r_mcangle_it	1.788
r_mcangle_other	1.787
r_scbond_it	1.639
r_scbond_other	1.638
r_angle_refined_deg	1.559
r_mcbond_other	1.354
r_mcbond_it	1.351
r_angle_other_deg	1.038
r_chiral_restr	0.116
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1212
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
ACORN	phasing