3LW5 | pdb_00003lw5

Improved model of plant photosystem I

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WSC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	22.5mM MES BIS-TRIS, 10mM SUCCINIC ACID, 6% PEG6000, 0.015% DTM, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.16	70.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.655	α = 90
b = 189.086	β = 91.24
c = 129.388	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	CCD	MARRESEARCH	MIRRORS	2009-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

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	3.3	30					82447

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2WSC	3.3	30	82447	4344	99.46	0.351	0.349	0.3529	0.383	0.3749	RANDOM	23.073

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]
-1.62		-1.43	-7.81		9.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.197
r_dihedral_angle_1_deg	26.852
r_dihedral_angle_3_deg	25.575
r_dihedral_angle_4_deg	22.066
r_angle_refined_deg	4.757
r_scangle_it	4.412
r_scbond_it	3.568
r_mcangle_it	0.612
r_chiral_restr	0.515
r_mcbond_it	0.416
r_bond_refined_d	0.023
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	24732
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	11638

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling