Experiment: 9SXB

Thermococcus sibiricus cyclic 2,3-diphosphoglycerate syntethase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8ORK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.5	292.15	The best diffracting crystals grew in condition A3 of the Morpheus screen consisting of 0.12 M divalents mix, 0.1 M Buffer System 1 pH 6.5 and 30% v/v Precipitant Mix 3 (https://calibrescientific.com/en/products/MDL-MD1-47 ).

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.46	α = 90
b = 80.56	β = 90
c = 82.74	γ = 90

Symmetry
Space Group	P 21 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	113.15	PIXEL	DECTRIS EIGER2 XE 16M		2023-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95374	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.28	73.83	100	1	11.6	13.7		50337

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	2.31	2.35	100		0.4		13

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	2.28	73.8	50336	2364	99.988	0.221	0.2186	0.2192	0.2782	0.2794	83.452

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]
-2.601			-3.984		6.584

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.714
r_dihedral_angle_6_deg	14.22
r_lrange_it	10.94
r_scangle_it	8.622
r_dihedral_angle_1_deg	7.956
r_dihedral_angle_2_deg	7.516
r_mcangle_it	7.255
r_scbond_it	5.886
r_mcbond_it	4.957
r_angle_refined_deg	1.766

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.714
r_dihedral_angle_6_deg	14.22
r_lrange_it	10.94
r_scangle_it	8.622
r_dihedral_angle_1_deg	7.956
r_dihedral_angle_2_deg	7.516
r_mcangle_it	7.255
r_scbond_it	5.886
r_mcbond_it	4.957
r_angle_refined_deg	1.766
r_nbtor_refined	0.296
r_nbd_refined	0.217
r_symmetry_nbd_refined	0.166
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.12
r_symmetry_xyhbond_nbd_refined	0.117
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6766
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	61

Software

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.