9KP0 | pdb_00009kp0

Crystal structure of Oryza sativa HPPD

X-RAY DIFFRACTION

---

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 acetate (pH 4.5), 20 vol% PEG1000, and 0.2 M zinc acetate 2 mM CoCl2

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.11	α = 101.387
b = 64.59	β = 107.961
c = 73.16	γ = 97

Symmetry
Space Group	P 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		2024-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.02	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	50	97.9	0.168	0.978	6.92	3.69		65758

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	2.12	95.3		0.842	0.622	2.03	3.32

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	45.94	65758	3288	98.328	0.195	0.1936	0.2013	0.2265	0.2308	28.281

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]
	-0.003	-0.002	-0.002	0.002	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.724
r_dihedral_angle_6_deg	13.676
r_dihedral_angle_2_deg	10.726
r_dihedral_angle_1_deg	6.782
r_lrange_it	5.744
r_lrange_other	5.656
r_scangle_it	3.776
r_scangle_other	3.775
r_mcangle_it	3.008
r_mcangle_other	3.008
r_scbond_it	2.279
r_scbond_other	2.279
r_mcbond_it	1.843
r_mcbond_other	1.839
r_angle_refined_deg	1.315
r_angle_other_deg	0.464
r_symmetry_xyhbond_nbd_refined	0.348
r_nbd_other	0.242
r_symmetry_nbd_refined	0.235
r_nbd_refined	0.2
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.172
r_xyhbond_nbd_other	0.138
r_metal_ion_refined	0.109
r_symmetry_metal_ion_refined	0.099
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.072
r_chiral_restr	0.062
r_gen_planes_refined	0.005
r_bond_refined_d	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	5995
Nucleic Acid Atoms
Solvent Atoms	497
Heterogen Atoms	18

Software

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