9GCE | pdb_00009gce

Ang-1 domain of the HupE/UreJ-2 protein from Rhodobacteraceae bacterium RbAng-1a with Cu bound

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	6.5	291	Zn sulfate, MES, polyethylene glycol monomethyl ether 550.

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.593	α = 90
b = 79.593	β = 90
c = 63.453	γ = 120

Symmetry
Space Group	P 32 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 EIGER2 XE 16M		2023-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97628	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.25	46.68	100	0.136	0.144	0.046	0.995	12.8	17.7		11371

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.25	2.32	100		1.626	1.732	0.593	0.618	2	16.2

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	2.25	46.68	11350	554	99.991	0.218	0.2158	0.2158	0.2554	0.2556	60.702

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]
1.609	0.804		1.609		-5.219

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.385
r_dihedral_angle_3_deg	12.193
r_lrange_other	9.037
r_lrange_it	9.031
r_scangle_it	8.484
r_scangle_other	8.479
r_dihedral_angle_1_deg	8.187
r_dihedral_angle_2_deg	7.903
r_scbond_it	7.085
r_scbond_other	7.045
r_mcangle_it	6.834
r_mcangle_other	6.831
r_mcbond_it	5.725
r_mcbond_other	5.721
r_angle_refined_deg	2.371
r_angle_other_deg	1.093
r_symmetry_nbd_refined	0.265
r_symmetry_xyhbond_nbd_refined	0.184
r_nbd_refined	0.178
r_xyhbond_nbd_refined	0.156
r_symmetry_nbd_other	0.145
r_nbtor_refined	0.136
r_nbd_other	0.117
r_chiral_restr	0.114
r_symmetry_metal_ion_refined	0.094
r_symmetry_nbtor_other	0.072
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1204
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	4

Software

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