4DP9 | pdb_00004dp9

The 1.00 Angstrom crystal structure of oxidized (CuII) poplar plastocyanin A at pH 6.0

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	6	277	2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.012	α = 90
b = 46.354	β = 90
c = 57.091	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	2002-02-21	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	15.99	96.9	0.045	19.2	3.5	42481	41152		2	5.84

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	1.02	80.7		0.26	3.5	2.9	2042

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	15.99	40686	39319	2096	96.64	0.12221	0.12109	0.13	0.14397	0.14	RANDOM	10.265

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]
0.06			-0.01		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.2
r_sphericity_free	13.637
r_dihedral_angle_3_deg	10.874
r_dihedral_angle_1_deg	7.443
r_scangle_it	6.921
r_sphericity_bonded	6.534
r_scbond_it	5.203
r_mcangle_it	3.279
r_rigid_bond_restr	2.742
r_angle_refined_deg	2.663
r_mcbond_it	2.528
r_nbd_refined	0.573
r_xyhbond_nbd_refined	0.504
r_symmetry_hbond_refined	0.385
r_nbtor_refined	0.329
r_symmetry_vdw_refined	0.262
r_chiral_restr	0.164
r_metal_ion_refined	0.069
r_bond_refined_d	0.027
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	738
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	1

Software

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