2O01 | pdb_00002o01

The Structure of a plant photosystem I supercomplex at 3.4 Angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	278	pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
4.15	70.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.054	α = 90
b = 188.784	β = 95.19
c = 127.518	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	100					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.875	ESRF	ID23-2

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	3.4	50	91.1	0.14	16.41	3.6		70551	3.4	3.4

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	3.4	3.52	78.9		0.475	3.4	2.7	6034

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	SAD	THROUGHOUT	PDB ENTRY 1QZV	3.4	40	69817	70551	3516	90.85	0.351	0.348	0.3528	0.409	0.4101	RANDOM	44.13

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]
-1.06		2.78	0.74		0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.946
r_dihedral_angle_3_deg	27.622
r_dihedral_angle_4_deg	20.588
r_dihedral_angle_1_deg	15.284
r_angle_refined_deg	4.101
r_scangle_it	1.697
r_scbond_it	1.334
r_mcangle_it	0.878
r_mcbond_it	0.563
r_symmetry_vdw_refined	0.411
r_nbd_refined	0.388
r_xyhbond_nbd_refined	0.337
r_nbtor_refined	0.334
r_chiral_restr	0.216
r_symmetry_hbond_refined	0.21
r_metal_ion_refined	0.113
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23599
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	6247

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing