7QQJ | pdb_00007qqj

Sucrose phosphorylase from Jeotgalibaca ciconiae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7QQI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	Protein was concentrated to 16 mg/ml in 25 mM Tris, pH 7.8, 100 mM NaCl. Drops were prepared by mixing protein and reservoir solution at a 1:1 volume ratio. Composition reservoir solution: 25% PEG 3350, 0.1 M Bis-tris propane, pH 6.5, 50 mM Na/K phosphate

Crystal Properties
Matthews coefficient	Solvent content
2.02	39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.639	α = 90
b = 90.828	β = 92.832
c = 96.17	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS3 2M		2021-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.96546	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.05	48	98.8	0.123	0.172	0.121	0.987	5.9	3		54973

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.11			0.908	1.269	0.885	0.336		2.8

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7QQI	2.05	48	54948	2719	98.669	0.199	0.1958	0.2	0.2544	0.26	31.144

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]
0.944		0.442	-0.56		-0.426

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.423
r_dihedral_angle_4_deg	18.546
r_dihedral_angle_3_deg	15.42
r_dihedral_angle_1_deg	7.14
r_lrange_it	6.462
r_lrange_other	6.45
r_scangle_it	4.99
r_scangle_other	4.99
r_mcangle_it	3.68
r_mcangle_other	3.68
r_scbond_it	3.251
r_scbond_other	3.25
r_mcbond_other	2.591
r_mcbond_it	2.59
r_angle_refined_deg	1.571
r_angle_other_deg	1.28
r_nbd_other	0.243
r_symmetry_nbd_refined	0.221
r_nbd_refined	0.202
r_symmetry_xyhbond_nbd_refined	0.192
r_symmetry_nbd_other	0.181
r_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.171
r_ncsr_local_group_1	0.106
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.074
r_symmetry_xyhbond_nbd_other	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7846
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms	8

Software

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