6EK9 | pdb_00006ek9

Cytosolic copper storage protein Csp from Streptomyces lividans: Cu loaded form

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	15 mg/ml protein. 1.4 M ammonium sulfate, 0.1 M MES pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.081	α = 90
b = 64.138	β = 90
c = 66.003	γ = 90

Symmetry
Space Group	I 2 2 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 PILATUS 6M	Mirrors	2016-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.976	ESRF	ID29

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	1.5	45.23	96.4	0.08	0.045	0.992	9.7	3.6		20701

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	1.5	1.53	96.6		0.161	0.097	0.958	4.5	3.5

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	6EIO	1.5	45.22	19471	1228	89.35	0.2071	0.2056	0.2117	0.2308	0.2279	RANDOM	37.874

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]
-7.89			0.64		7.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.198
r_dihedral_angle_4_deg	21.717
r_dihedral_angle_3_deg	17.075
r_sphericity_free	5.045
r_dihedral_angle_1_deg	4.553
r_sphericity_bonded	4.049
r_rigid_bond_restr	3.947
r_angle_refined_deg	2.056
r_angle_other_deg	1.247
r_chiral_restr	0.127
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	859
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Aimless	data reduction
Coot	model building
PHASER	phasing