4YKB | pdb_00004ykb

Structure of GUN4 from Chlamydomonas reinhardtii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Z3X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	1:1 ratio of protein (35 mg/mL in 20 mM Tricine (pH 8.0), 2 mM beta-mercaptoethanol) to well solution (1.0 M ammonium citrate (pH 7.0), 0.1 M Bis Tris Propane (pH 7.0). Crystals only appeared after 44 weeks, likely the time taken for proteolysis, resulting in the N- and C-terminal truncations

Crystal Properties
Matthews coefficient	Solvent content
2.64	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.998	α = 90
b = 114.998	β = 90
c = 141.193	γ = 120

Symmetry
Space Group	P 32 2 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	ADSC QUANTUM 315r		2014-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

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	3.5	44.56	99.1	0.21	5.2	3.5		13965			78

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	3.5	3.83	99		0.666	1.9	3.6

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	1Z3X	3.5	44.5	13187	753	99.05	0.25907	0.25602	0.2548	0.31315	0.3089	RANDOM	57.378

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]
-0.55	-0.28		-0.55		1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.429
r_dihedral_angle_3_deg	16.219
r_dihedral_angle_4_deg	12.238
r_long_range_B_refined	12.079
r_long_range_B_other	12.079
r_scangle_other	6.439
r_mcangle_it	6.389
r_mcangle_other	6.388
r_dihedral_angle_1_deg	6.352
r_scbond_it	3.999
r_scbond_other	3.998
r_mcbond_it	3.979
r_mcbond_other	3.978
r_angle_other_deg	1.578
r_angle_refined_deg	1.466
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_bond_other_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6241
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing