9FJ8 | pdb_00009fj8

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

X-RAY DIFFRACTION

---

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		285	1.4M Ammonium Sulphate 0.2M NaCl 0.1M Na Cacodylate pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
6.73	81.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.338	α = 90
b = 137.338	β = 90
c = 168.951	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	50	100	0.107	0.996	5.2	8.1		82187

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			0.56	0.925

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	48.675	82136	4054	99.95	0.17	0.1693	0.1756	0.1844	0.1881	34.006

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]
0.645	0.323		0.645		-2.094

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.556
r_dihedral_angle_6_deg	12.871
r_dihedral_angle_1_deg	7.281
r_dihedral_angle_2_deg	5.147
r_lrange_it	4.446
r_lrange_other	4.056
r_scangle_other	2.599
r_scangle_it	2.595
r_mcangle_it	1.848
r_mcangle_other	1.848
r_scbond_it	1.479
r_scbond_other	1.479
r_angle_refined_deg	1.085
r_mcbond_it	1.07
r_mcbond_other	1.069
r_angle_other_deg	0.425
r_symmetry_nbd_other	0.205
r_nbd_refined	0.176
r_nbtor_refined	0.173
r_nbd_other	0.116
r_xyhbond_nbd_refined	0.108
r_symmetry_xyhbond_nbd_refined	0.09
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.052
r_ncsr_local_group_1	0.052
r_symmetry_nbd_refined	0.034
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4807
Nucleic Acid Atoms
Solvent Atoms	577
Heterogen Atoms	117

Software

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