2GIM | pdb_00002gim

1.6 Angstrom structure of plastocyanin from Anabaena variabilis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BAW	PDB Entry: 1BAW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	300	1.15 M trisodium citrate, 7.67 mM sodium borate buffer pH 8.5 , VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.85	α = 90
b = 45.81	β = 90
c = 63.41	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	CCD	MARRESEARCH		2005-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711	1.11	MAX II	I711

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.55	20	93.3				24943

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.55	1.8	99.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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: 1BAW	1.6	19.19	23695	23695	1248	93.3	0.21138	0.21138	0.20881	0.2143	0.26021	0.2607	RANDOM	18.278

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]
-0.48			-0.39		0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.888
r_dihedral_angle_3_deg	15.041
r_dihedral_angle_4_deg	8.206
r_dihedral_angle_1_deg	6.572
r_scangle_it	2.74
r_mcangle_it	2.164
r_scbond_it	1.931
r_angle_refined_deg	1.859
r_mcbond_it	1.571
r_nbtor_refined	0.331
r_nbd_refined	0.242
r_symmetry_hbond_refined	0.241
r_xyhbond_nbd_refined	0.22
r_symmetry_vdw_refined	0.186
r_chiral_restr	0.117
r_metal_ion_refined	0.043
r_bond_refined_d	0.018
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1600
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
MOLREP	phasing