9GCB | pdb_00009gcb

DUF4198 protein from Ideonella sakaiensis with Ni 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	7	291	Na malonate, HEPES, Jeffamine D2001

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.532	α = 81.421
b = 47.468	β = 81.502
c = 49.452	γ = 83.599

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	100	PIXEL	DECTRIS EIGER2 XE 16M		2021-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.44	48.46	64.1	0.033	0.046	0.033	0.998	18.2	3.3		44708

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)
	1.44	1.47	4.1		0.157	0.221	0.157	0.909	1.9	1.2

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	1.44	48.46	44705	2199	64.128	0.132	0.1296	0.1296	0.1824	0.1824	15.519

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]
0.259	-0.03	1.472	-0.845	-0.886	0.725

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.561
r_dihedral_angle_3_deg	11.655
r_lrange_it	11.628
r_dihedral_angle_2_deg	9.515
r_scangle_it	6.508
r_dihedral_angle_1_deg	6.069
r_mcangle_it	4.696
r_scbond_it	4.558
r_rigid_bond_restr	4.193
r_mcbond_it	3.196
r_angle_refined_deg	1.751
r_nbtor_refined	0.311
r_symmetry_nbd_refined	0.215
r_nbd_refined	0.198
r_symmetry_xyhbond_nbd_refined	0.174
r_xyhbond_nbd_refined	0.165
r_chiral_restr	0.123
r_ncsr_local_group_1	0.117
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3112
Nucleic Acid Atoms
Solvent Atoms	480
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
REFMAC	phasing