3A1D | pdb_00003a1d

Crystal structure of the P- and N-domains of CopA, a copper-transporting P-type ATPase, bound with ADP-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		5.5	283	pH 5.5, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.956	α = 90
b = 89.956	β = 90
c = 190.375	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		2007-07-11	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	99.9	0.129	30.6	3.6		63866			41

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	100		0.483	5.8	3.4

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	63866	3413	99.79	0.19379	0.19213	0.19	0.22563	0.22	RANDOM	41.004

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]
0.09			0.09		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.56
r_dihedral_angle_4_deg	17.486
r_dihedral_angle_3_deg	12.735
r_dihedral_angle_1_deg	5.227
r_scangle_it	3.61
r_scbond_it	2.174
r_mcangle_it	1.312
r_angle_refined_deg	1.285
r_mcbond_it	0.81
r_nbtor_refined	0.295
r_metal_ion_refined	0.257
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.199
r_xyhbond_nbd_refined	0.191
r_symmetry_hbond_refined	0.143
r_chiral_restr	0.079
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	4033
Nucleic Acid Atoms
Solvent Atoms	555
Heterogen Atoms	56

Software

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