9KOZ | pdb_00009koz

Crystal structure of Arabidopsis thaliana 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), 32 or 28 vol% polyethylene glycol (PEG) 400, and 15 or 10 vol% 2-propanol 2 mM iptriazopyrid and 2 mM CoCl2

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.16	α = 90
b = 96.04	β = 92.806
c = 97.82	γ = 90

Symmetry
Space Group	P 1 21 1

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		2023-12-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.025	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	2.15	50	99.7	0.239	0.991	6.14	6.69		96459

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	2.15	2.28	98.9		2.988	0.421	0.6	5.63

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	2.15	48.022	94904	4744	98.139	0.214	0.211	0.2176	0.2662	0.2687	49.468

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]
0.022		0.001	-0.006		-0.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.077
r_dihedral_angle_3_deg	15.182
r_dihedral_angle_6_deg	13.024
r_dihedral_angle_other_2_deg	12.612
r_lrange_it	8.334
r_lrange_other	8.329
r_dihedral_angle_1_deg	6.722
r_scangle_it	5.723
r_scangle_other	5.723
r_mcangle_it	4.937
r_mcangle_other	4.936
r_scbond_it	3.681
r_scbond_other	3.681
r_mcbond_it	3.179
r_mcbond_other	3.179
r_angle_refined_deg	1.24
r_angle_other_deg	0.438
r_nbd_other	0.231
r_symmetry_nbd_other	0.204
r_nbd_refined	0.203
r_symmetry_nbd_refined	0.196
r_symmetry_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.135
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.057
r_symmetry_xyhbond_nbd_other	0.028
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12352
Nucleic Acid Atoms
Solvent Atoms	388
Heterogen Atoms	120

Software

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