8QJ0 | pdb_00008qj0

Room-temperature Serial Synchrotron Crystallography structure of Spinacia oleracea RuBisCO

X-RAY DIFFRACTION

---

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AUS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	SpRub solution at a concentration of 15 mg/mL (in a buffer of 20 mM HEPES, 5 mM MgCl2, pH 8.0), combined reservoir solution (0.2 M MgCl2x6H2O, 0.1 M Tris pH 7.0, 12% w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.6	α = 90
b = 157.12	β = 90
c = 202.74	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS EIGER X 4M		2022-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.976	PETRA III, EMBL c/o DESY	P14 (MX2)

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		fixed target

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (All)	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	2.3	97.78	100	0.9943	0.0952	7.96	770		112061

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.382	100		0.9523	0.2388	3.66	528

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	97.78	111898	5444	99.893	0.183	0.1811	0.1811	0.2274	0.2274	25.303

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]
0.206			0.652		-0.858

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.912
r_dihedral_angle_3_deg	13.956
r_dihedral_angle_2_deg	10.485
r_lrange_it	7.989
r_lrange_other	7.977
r_dihedral_angle_1_deg	7.886
r_scangle_it	6.528
r_scangle_other	6.528
r_mcangle_it	4.745
r_mcangle_other	4.745
r_scbond_other	4.216
r_scbond_it	4.215
r_mcbond_it	3.146
r_mcbond_other	3.146
r_angle_refined_deg	2.149
r_angle_other_deg	1.034
r_nbd_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.16
r_symmetry_nbd_other	0.138
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.123
r_symmetry_nbd_refined	0.103
r_nbd_other	0.091
r_ncsr_local_group_3	0.081
r_ncsr_local_group_5	0.077
r_ncsr_local_group_9	0.07
r_ncsr_local_group_12	0.07
r_symmetry_nbtor_other	0.068
r_ncsr_local_group_2	0.068
r_ncsr_local_group_6	0.068
r_ncsr_local_group_7	0.066
r_ncsr_local_group_11	0.065
r_ncsr_local_group_4	0.064
r_ncsr_local_group_1	0.062
r_ncsr_local_group_8	0.061
r_ncsr_local_group_10	0.057
r_symmetry_xyhbond_nbd_other	0.042
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17873
Nucleic Acid Atoms
Solvent Atoms	995
Heterogen Atoms	16

Software

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