5ARN | pdb_00005arn

Cu(I)-CSP3 (COPPER STORAGE PROTEIN 3) FROM METHYLOSINUS

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ARM	PDB ENTRY 5ARM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				75 MM MGCL2, 100 MM HEPES PH 7.5, AND 34% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.51	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.902	α = 90
b = 105.902	β = 90
c = 45.63	γ = 90

Symmetry
Space Group	I 41 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		2013-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.3	41.91	99.7	0.08	6.3	4.1		5998		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	99.9		0.65	1.9	1.9

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	PDB ENTRY 5ARM	2.3	74.88	5534	306	96.98	0.18912	0.18573	0.2	0.24274	0.23	RANDOM	50.733

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]
2.14			2.14		-4.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.731
r_dihedral_angle_3_deg	14.792
r_dihedral_angle_4_deg	14.265
r_dihedral_angle_1_deg	5.688
r_mcangle_it	4.876
r_scbond_it	4.102
r_mcbond_it	3.534
r_mcbond_other	3.534
r_angle_refined_deg	1.494
r_angle_other_deg	1.025
r_chiral_restr	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	838
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	19

Software

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