9IRJ | pdb_00009irj

X-ray structure of PSmOrange3 (trigonal form)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Q7T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	Na/K Phosphate

Crystal Properties
Matthews coefficient	Solvent content
5.61	78.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.165	α = 90
b = 137.165	β = 90
c = 55.223	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 EIGER X 16M		2023-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.979183	SSRF	BL10U2

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	2.8	68.59	100	0.98	6.3	19.1		15169

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	2.8	2.94			0.7

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	2.8	68.59	14009	651	93.599	0.18	0.1783	0.1854	0.2099	0.1857	55.401

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]
-0.164	-0.082		-0.164		0.533

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.684
r_dihedral_angle_3_deg	20.469
r_dihedral_angle_4_deg	18.965
r_lrange_other	14.917
r_lrange_it	14.911
r_scangle_it	11.677
r_scangle_other	11.673
r_dihedral_angle_1_deg	8.32
r_scbond_it	7.599
r_scbond_other	7.596
r_mcangle_it	6.625
r_mcangle_other	6.624
r_mcbond_it	4.551
r_mcbond_other	4.485
r_angle_refined_deg	2.193
r_angle_other_deg	1.347
r_nbd_refined	0.208
r_symmetry_nbd_other	0.205
r_nbtor_refined	0.185
r_nbd_other	0.181
r_xyhbond_nbd_refined	0.159
r_symmetry_nbtor_other	0.105
r_chiral_restr	0.074
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_symmetry_nbd_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1715
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	22

Software

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