2CJ3 | pdb_00002cj3

CRYSTAL STRUCTURE OF PLASTOCYANIN FROM A CYANOBACTERIUM, ANABAENA VARIABILIS

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PLC	PDB ENTRY 1PLC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	288	PEG6000, HEPES, POTASSIUM PHOSPHATE, SODIUM PHOSPHATE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 288K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.29	α = 90
b = 68.48	β = 109.97
c = 42.26	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	DIFFRACTOMETER	NRAF-NONIUS CAD4	GRAPHITE MONOCHROMATOR MIRROR AND SI(111)	1988-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	PHILIPS

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	1.5	10	80.1	0.08				21041		2	11

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	1.5	1.6	24.9		0.37

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1PLC	1.7	39.84	17228	923	82.3	0.141	0.14	0.163	RANDOM	16.56

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]
0.15		-0.17	-0.2		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.724
r_dihedral_angle_3_deg	14.452
r_scangle_it	7.115
r_dihedral_angle_4_deg	6.936
r_dihedral_angle_1_deg	6.197
r_scbond_it	5.64
r_mcangle_it	3.082
r_mcbond_it	2.629
r_angle_refined_deg	1.434
r_angle_other_deg	0.719
r_nbd_refined	0.193
r_nbtor_refined	0.181
r_nbd_other	0.165
r_symmetry_hbond_refined	0.128
r_symmetry_vdw_other	0.122
r_xyhbond_nbd_refined	0.11
r_symmetry_vdw_refined	0.092
r_nbtor_other	0.086
r_chiral_restr	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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	1564
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
WEIS	data reduction
PROTEIN	data scaling
MERLOT	phasing