9FJZ | pdb_00009fjz

Teth514_1788 1,2-beta-oligomannan phosphorylase in complex with mannoheptaose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	SwissModel

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	290	0.8M Na Citrate 0.1M Na Cacodylater pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
6.55	81.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.11	α = 90
b = 137.11	β = 90
c = 168.638	γ = 120

Symmetry
Space Group	P 32 2 1

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		2019-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9793	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	50	100	0.09	0.998	6.5	7.2		81687

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	2.3	2.42			0.734	0.83

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.3	44.92	81662	4081	99.917	0.169	0.1683	0.1741	0.1751	0.1816	39.083

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]
0.177	0.089		0.177		-0.576

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	11.017
r_dihedral_angle_3_deg	9.745
r_dihedral_angle_1_deg	6.999
r_lrange_it	5.97
r_lrange_other	5.866
r_dihedral_angle_2_deg	4.313
r_scangle_it	3.146
r_scangle_other	3.145
r_mcangle_it	2.14
r_mcangle_other	2.14
r_scbond_it	1.78
r_scbond_other	1.78
r_mcbond_it	1.248
r_mcbond_other	1.248
r_angle_refined_deg	0.871
r_angle_other_deg	0.376
r_symmetry_nbd_other	0.21
r_nbtor_refined	0.172
r_nbd_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.14
r_symmetry_nbd_refined	0.117
r_xyhbond_nbd_refined	0.109
r_nbd_other	0.099
r_symmetry_nbtor_other	0.079
r_ncsr_local_group_1	0.046
r_chiral_restr	0.04
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4814
Nucleic Acid Atoms
Solvent Atoms	515
Heterogen Atoms	179

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing