9KOY | pdb_00009koy

Crystal structure of Oryza sativa HPPD complexed with iptriazopyrid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SP9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M sodium citrate (pH 5.0), 12 weight% PEG6000, and 50 mM sodium iodide 2 mM iptriazopyrid and 2 mM CoCl2

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.61	α = 90
b = 158.61	β = 90
c = 84.075	γ = 90

Symmetry
Space Group	P 42 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	95	PIXEL	DECTRIS EIGER X 4M		2024-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.018	Photon Factory	BL-1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.9	50	99.8	0.26	0.997	12.39	13.4		24533

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.06	99.3		3.084	0.379	0.89	13.9

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	1SP9	2.9	46.652	24333	1217	99.947	0.207	0.2033	0.2114	0.2855	0.2833	78.673

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]
0.001			0.001		-0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_2_deg	19.189
r_dihedral_angle_3_deg	17.548
r_dihedral_angle_2_deg	16.275
r_lrange_other	13.962
r_lrange_it	13.961
r_dihedral_angle_6_deg	12.85
r_scangle_it	9.814
r_scangle_other	9.813
r_mcangle_it	9.309
r_mcangle_other	9.308
r_dihedral_angle_1_deg	7.069
r_scbond_it	6.108
r_scbond_other	6.107
r_mcbond_it	5.837
r_mcbond_other	5.833
r_angle_refined_deg	1.457
r_angle_other_deg	0.522
r_metal_ion_refined	0.284
r_nbd_refined	0.222
r_nbd_other	0.215
r_symmetry_nbd_other	0.211
r_symmetry_nbd_refined	0.186
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_refined	0.153
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.066
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5847
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	64

Software

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