6IBI | pdb_00006ibi

Copper binding protein from Laetisaria arvalis (LaX325)

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	MRC plates with 1:1 ratio drops (enzyme:reservoir solution) and 100 ul reservoir using an Oryx-8 robot. Protein: 13.3 mg/ml in 20 mM MES pH 6.0. Reservoir: 20 mM L-Na-Glutamate, 20 mM DL-Alanine (racemic), 20 mM Glycine, 20 mM DL-Lysine HCl (racemic), 20 mM DL-Serine (racemic), 50 mM MES monohydrate pH 6.5, 50 mM imidazole pH 6.5. 20% (w/v) PEG 500 MME and 10% (w/v) PEG 20000.

Crystal Properties
Matthews coefficient	Solvent content
3.42	64.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.599	α = 90
b = 84.635	β = 90
c = 127.319	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS 6M-F		2018-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.299	ESRF	ID29

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	2.08	100	99.6	0.152	0.998	12.93	14		57268		-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	2.08	2.13	98.5		1.398	0.744	1.07	14.3

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.08	42.35	52714	2641	99.53	0.2454	0.24417	0.2504	0.27087	0.275	RANDOM	43.444

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]
1.04			1.78		-2.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.884
r_dihedral_angle_3_deg	13.254
r_dihedral_angle_4_deg	11.447
r_long_range_B_other	8.353
r_long_range_B_refined	8.352
r_dihedral_angle_1_deg	6.698
r_scangle_other	6.226
r_mcangle_it	4.833
r_mcangle_other	4.832
r_scbond_it	4.237
r_scbond_other	4.237
r_mcbond_it	3.448
r_mcbond_other	3.446
r_angle_other_deg	2.412
r_angle_refined_deg	1.383
r_chiral_restr	0.063
r_gen_planes_other	0.047
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
r_bond_other_d	0.002
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	4569
Nucleic Acid Atoms
Solvent Atoms	549
Heterogen Atoms	386

Software

Software
Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing
AutoSol	phasing
PHASER	phasing
Coot	model building