3FYD | pdb_00003fyd

Crystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QYR	composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9
experimental model	PDB	2H1R	composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9
experimental model	PDB	1ZQ9	composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	293	PEG 8000 (14-16%), 25 mM MES, 50 MM NH2SO4, 7 mM MgCl2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.236	α = 90
b = 65.906	β = 108.1
c = 61.932	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	IMAGE PLATE	RIGAKU RAXIS IV	Rigaku Varimax Confocal Optics	2008-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	1.75	33.1	94.4	0.038	29.1	7.06	31119	29365			38.9

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)
	1.75	1.81	91.1		0.294	4.9	6.98	3079

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9	1.75	22	31106	26413	2926	94.37	0.18126	0.17624	0.21	0.22643	RANDOM	43.95

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]
-0.07		-0.42	-0.48		0.3

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_2_deg	32.708
f_dihedral_angle_4_deg	14.768
f_dihedral_angle_3_deg	14.475
f_scangle_it	9.584
f_scbond_it	8.044
f_dihedral_angle_1_deg	5.679
f_mcangle_it	4.87
f_mcbond_it	4.041
f_angle_refined_deg	1.133
f_nbtor_refined	0.304
f_nbd_refined	0.197
f_symmetry_vdw_refined	0.188
f_symmetry_hbond_refined	0.133
f_xyhbond_nbd_refined	0.127
f_chiral_restr	0.09
f_bond_refined_d	0.011
f_gen_planes_refined	0.005
f_bond_other_d
f_angle_other_deg
f_gen_planes_other
f_nbd_other
f_nbtor_other
f_xyhbond_nbd_other
f_metal_ion_refined
f_metal_ion_other
f_symmetry_vdw_other
f_symmetry_hbond_other
f_symmetry_metal_ion_refined
f_symmetry_metal_ion_other
f_mcbond_other
f_rigid_bond_restr
f_sphericity_free
f_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2177
Nucleic Acid Atoms
Solvent Atoms	333
Heterogen Atoms	25

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
CrystalClear	data reduction
CrystalClear	data scaling