6IBJ | pdb_00006ibj

Copper binding protein from Laetisaria arvalis (LaX325)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6IBI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	20 mM L-Na-Glutamate, 20 mM DL-Alanine (racemic), 20 mM Glycine, 20 mM DL-Lysine HCl (racemic), 20 mM DL-Serine (racemic) 100 mM MES monohydrate pH 6.5 / 100 mM imidazole pH 6.5 20% (w/v) PEG 500 MME and 10% (w/v) PEG 20.000.

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.92	α = 90
b = 74.92	β = 90
c = 64.39	γ = 90

Symmetry
Space Group	P 43 21 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	Kirkpatrick-Baez (KB) mirror pair (VFM, HFM)	2018-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9799	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.1	60	99.9	0.087	0.999	12.25	7.2		11173		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.15	99.9		0.1703	0.803	1.49	7.44

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6IBI	2.1	48.88	10600	575	99.85	0.19647	0.19351	0.2	0.25618	0.26	RANDOM	54.919

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]
2.2			2.2		-4.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.247
r_dihedral_angle_4_deg	12.578
r_dihedral_angle_3_deg	12.387
r_long_range_B_other	8.203
r_long_range_B_refined	8.201
r_dihedral_angle_1_deg	7.232
r_scangle_other	6.714
r_mcangle_it	5.304
r_mcangle_other	5.302
r_scbond_it	4.654
r_scbond_other	4.65
r_mcbond_it	3.769
r_mcbond_other	3.767
r_angle_refined_deg	1.255
r_angle_other_deg	0.823
r_chiral_restr	0.054
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1125
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing