3A1C | pdb_00003a1c

crystal structure of the P- and N-domains of CopA, a copper-transporting P-type ATPase, bound with AMPPCP-Mg

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B8E	PDB ENTRY 2B8E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	283	5% PEG 6000, 1.5M NaCl, 0.1M MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.787	α = 90
b = 90.787	β = 90
c = 191.788	γ = 90

Symmetry
Space Group	P 43 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	CCD	ADSC QUANTUM 315		2007-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.9	SPring-8	BL41XU

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	1.85	20	99.6	0.081	33.7	6.2		65461			44.9

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	1.85	1.9	99.1		0.291	2.8	6.2

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 2B8E	1.85	20	65461	3500	99.76	0.19675	0.19526	0.19	0.22501	0.22	RANDOM	44.895

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]
0.17			0.17		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.223
r_dihedral_angle_4_deg	19.17
r_dihedral_angle_3_deg	13.589
r_dihedral_angle_1_deg	5.305
r_scangle_it	3.739
r_scbond_it	2.256
r_mcangle_it	1.388
r_angle_refined_deg	1.341
r_mcbond_it	0.849
r_nbtor_refined	0.297
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.195
r_symmetry_vdw_refined	0.17
r_symmetry_hbond_refined	0.111
r_chiral_restr	0.087
r_metal_ion_refined	0.02
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4037
Nucleic Acid Atoms
Solvent Atoms	473
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing