9QVW | pdb_00009qvw

Nostoc sp. 3335mg GT108 family enzyme native

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	0.1 M Bis-Tris pH 6.5 and 28% (w/v) PEG MME 2000

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.65	α = 90
b = 130.65	β = 90
c = 47.3	γ = 90

Symmetry
Space Group	P 43 21 2

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		2020-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	1.0	Diamond	I24

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	1.45	65.32	100	0.079	0.082	0.023	0.999	20	25.1		72944

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)
	1.45	1.47	99.9		2.051	2.132	0.582	0.656	1.7	25.9

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	1.45	65.32	72875	3592	99.995	0.169	0.1685	0.1685	0.1864	0.1865	27.475

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]
0.163			0.163		-0.326

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.204
r_dihedral_angle_3_deg	11.31
r_dihedral_angle_2_deg	9.366
r_dihedral_angle_1_deg	7.188
r_lrange_it	6.674
r_lrange_other	6.594
r_scangle_it	4.888
r_scangle_other	4.886
r_mcangle_it	3.43
r_mcangle_other	3.429
r_scbond_it	3.384
r_scbond_other	3.383
r_mcbond_other	2.407
r_mcbond_it	2.405
r_angle_refined_deg	1.91
r_angle_other_deg	0.664
r_nbd_refined	0.207
r_nbd_other	0.201
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.159
r_symmetry_nbd_refined	0.126
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2365
Nucleic Acid Atoms
Solvent Atoms	340
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
MOLREP	phasing