9GOJ | pdb_00009goj

Crystal structure of HpeI from Rhodococcus rhodochrous GD02

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	25% PEG 1500, 0.1 M PCTP (Sodium propionate, Sodium cacodylate trihydrate, Bis-Tris propane) pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.902	α = 90
b = 57.27	β = 99.591
c = 67.118	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	100	PIXEL	DECTRIS EIGER2 XE 16M		2023-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.803	66.18	90.7	0.164	0.067	0.996	6.9	7		14742

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.803	1.972	66		1.312	0.528	0.642	1.4	7.2

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	1.803	66.18	14742	715	46.353	0.21	0.2072	0.2074	0.2552	0.2546	24.712

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]
-0.256		0.07	-0.057		0.274

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.841
r_dihedral_angle_6_deg	14.655
r_dihedral_angle_1_deg	7.501
r_dihedral_angle_2_deg	6.976
r_lrange_it	6.022
r_scangle_it	3.656
r_mcangle_it	2.751
r_scbond_it	2.317
r_angle_refined_deg	1.778
r_mcbond_it	1.686
r_nbtor_refined	0.304
r_symmetry_nbd_refined	0.254
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.197
r_chiral_restr	0.125
r_symmetry_xyhbond_nbd_refined	0.12
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2541
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing