9PVQ | pdb_00009pvq

Crystal structure of HpsO from Cupriavidus pinatubonensis, crystal form 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q46N54-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	15-22% PEG4000, 0.2 M ammonium acetate, 0.1 M sodium acetate (pH 5.5)

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.72	α = 90
b = 58.72	β = 90
c = 271.48	γ = 90

Symmetry
Space Group	I 41 2 2

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		2022-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

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	1.08	41.56	98.1	1	24.3	15.3		99955

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	1.08	1.11			0.95

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	1.08	41.556	99953	4984	97.834	0.12	0.1191	0.1188	0.1358	0.1351	13.826

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]
0.433			0.433		-0.865

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.425
r_rigid_bond_restr	16.733
r_lrange_it	14.124
r_scbond_it	13.726
r_scbond_other	13.72
r_scangle_it	13.167
r_scangle_other	13.162
r_lrange_other	12.902
r_dihedral_angle_3_deg	11.495
r_dihedral_angle_1_deg	6.636
r_dihedral_angle_2_deg	6.083
r_mcangle_it	6.079
r_mcangle_other	6.077
r_mcbond_it	4.387
r_mcbond_other	4.381
r_angle_refined_deg	1.786
r_angle_other_deg	0.655
r_nbd_refined	0.28
r_xyhbond_nbd_refined	0.248
r_symmetry_nbd_refined	0.248
r_symmetry_nbd_other	0.193
r_nbd_other	0.188
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.132
r_chiral_restr	0.106
r_symmetry_nbtor_other	0.077
r_symmetry_xyhbond_nbd_other	0.05
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1840
Nucleic Acid Atoms
Solvent Atoms	264
Heterogen Atoms	8

Software

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