5JU9 | pdb_00005ju9

Structure of a beta-1,4-mannanase, SsGH134, in complex with Man3.

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, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.68	α = 90
b = 53.63	β = 90
c = 82.14	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 PILATUS3 6M		2016-02-01	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)	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	1.18	44.91	97.5	16.6	7		52763

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	1.18	1.21	80.2		0.558	2.4	3.7

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	alpha-helical fragment	1.18	44.91	50049	2647	97.39	0.1325	0.13143	0.13	0.15313	0.13	RANDOM	13.909

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]
0.09			0.11		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.944
r_sphericity_free	28.502
r_dihedral_angle_4_deg	23.61
r_dihedral_angle_3_deg	11.877
r_sphericity_bonded	7.764
r_dihedral_angle_1_deg	5.096
r_long_range_B_refined	2.689
r_long_range_B_other	2.688
r_scangle_other	2.158
r_scbond_it	1.702
r_scbond_other	1.701
r_mcangle_it	1.604
r_mcangle_other	1.603
r_angle_refined_deg	1.574
r_rigid_bond_restr	1.492
r_mcbond_it	1.247
r_mcbond_other	1.247
r_angle_other_deg	1.062
r_chiral_restr	0.107
r_bond_refined_d	0.012
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	1230
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	36

Software

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