4DP5 | pdb_00004dp5

The 1.88 Angstrom crystal structure of oxidized (CuII) poplar plastocyanin B at pH 8.0

X-RAY DIFFRACTION

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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, HANGING DROP	8	277	2.6 M ammonium sulfate, 0.1 M sodium acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.913	α = 90
b = 46.246	β = 90
c = 52.648	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	MAR CCD 165 mm	mirrors	2002-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.05	MPG/DESY, HAMBURG	BW6

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	1.88	14.74	100	0.114	16.9	7	6614	6611		2	18.27

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	1.88	1.91	99.1		0.471	2.8	6.8	320

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 (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 1PLC	1.88	14.74	6356	6258	311	98.46	0.15815	0.15391	0.16	0.24784	0.24	RANDOM	20.915

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]
-1.77			0.17		1.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.905
r_dihedral_angle_3_deg	16.612
r_dihedral_angle_1_deg	6.437
r_scangle_it	5.059
r_scbond_it	3.432
r_angle_refined_deg	2.008
r_mcangle_it	1.931
r_mcbond_it	1.269
r_nbtor_refined	0.316
r_nbd_refined	0.233
r_symmetry_vdw_refined	0.222
r_xyhbond_nbd_refined	0.207
r_symmetry_hbond_refined	0.171
r_chiral_restr	0.132
r_metal_ion_refined	0.027
r_bond_refined_d	0.023
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_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	737
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	12

Software

Software
Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling