9PVR | pdb_00009pvr

Crystal structure of HpsO from Cupriavidus pinatubonensis, crystal form 2

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	20 - 22% PEG4000, 0.2 M sodium chloride or lithium chloride, 0.1 M Tris-HCl (pH 8.0)

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.684	α = 90
b = 122.176	β = 117.099
c = 51.314	γ = 90

Symmetry
Space Group	C 1 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		2023-03-04	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	37.51	99.3	1	13.3	3.4		184643

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			0.91

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	37.509	184642	9472	99.23	0.118	0.1175	0.1173	0.1349	0.1345	11.698

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		-0.078	0.029		0.036

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.621
r_dihedral_angle_3_deg	12.127
r_lrange_it	12.033
r_lrange_other	11.156
r_dihedral_angle_2_deg	10.558
r_scangle_it	7.891
r_scangle_other	7.89
r_mcangle_it	7.338
r_mcangle_other	7.337
r_dihedral_angle_1_deg	6.548
r_mcbond_it	6.23
r_mcbond_other	6.229
r_scbond_it	5.321
r_scbond_other	5.32
r_rigid_bond_restr	4.114
r_angle_refined_deg	1.813
r_angle_other_deg	0.655
r_nbd_refined	0.376
r_symmetry_nbd_other	0.24
r_symmetry_xyhbond_nbd_refined	0.233
r_nbtor_refined	0.205
r_nbd_other	0.175
r_xyhbond_nbd_refined	0.159
r_symmetry_nbd_refined	0.118
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.01
r_gen_planes_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	3582
Nucleic Acid Atoms
Solvent Atoms	408
Heterogen Atoms	8

Software

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