9GQS | pdb_00009gqs

Teth514_1788 1,2-beta-oligomannan phosphorylase in complex with mannose (+1) and phosphate

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, SITTING DROP		285	0.1 M Sodium cacodylate trihydrate pH 6.5, 1.0 M Sodium citrate tribasic dihydrate

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.269	α = 90
b = 137.269	β = 90
c = 169.384	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		2018-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.9677	ESRF	MASSIF-1

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	2.5	50	99.8	0.112	0.996	6.4	5.7		64153

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64			0.757

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	2.5	44.972	64104	3113	99.763	0.152	0.1505	0.1609	0.1721	0.1783	34.922

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]
0.017	0.009		0.017		-0.056

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.476
r_dihedral_angle_3_deg	12.966
r_lrange_it	8.231
r_lrange_other	8.23
r_dihedral_angle_1_deg	7.517
r_scangle_it	6.445
r_scangle_other	6.444
r_dihedral_angle_2_deg	5.76
r_scbond_it	3.904
r_scbond_other	3.903
r_mcangle_it	3.093
r_mcangle_other	3.093
r_mcbond_it	2
r_mcbond_other	2
r_angle_refined_deg	1.293
r_angle_other_deg	0.468
r_symmetry_nbd_other	0.194
r_nbd_refined	0.181
r_nbd_other	0.179
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.146
r_symmetry_xyhbond_nbd_refined	0.13
r_symmetry_nbd_refined	0.123
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.062
r_ncsr_local_group_1	0.057
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4807
Nucleic Acid Atoms
Solvent Atoms	652
Heterogen Atoms	76

Software

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