1YCY | pdb_00001ycy

Conserved hypothetical protein Pfu-1806301-001 from Pyrococcus furiosus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5	291	20% w/v PEG 3000, 0.1M sodium acetate, 0.01M NAD, pH 4.5, modified microbatch, temperature 291K, pH 4.50

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.958	α = 90
b = 82.958	β = 90
c = 189.782	γ = 120

Symmetry
Space Group	P 62 2 2

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	MARMOSAIC 225 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-ID

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	2.67	50	95	0.089				11111

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)
	2.67	2.77	61.6		0.294

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAS	THROUGHOUT	2.8	20	10016	518	100	0.281	0.302	0.311	0.3198	THIN SHELLS	55.52

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]
3.246	1.623		3.246		-4.869

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.344
r_dihedral_angle_4_deg	22.463
r_dihedral_angle_3_deg	16.832
r_dihedral_angle_1_deg	6.453
r_mcangle_it	3.401
r_scangle_it	2.848
r_mcbond_it	2.651
r_scbond_it	1.949
r_angle_refined_deg	1.343
r_angle_other_deg	0.738
r_mcbond_other	0.636
r_symmetry_vdw_refined	0.236
r_nbd_refined	0.221
r_symmetry_vdw_other	0.196
r_nbtor_refined	0.183
r_nbd_other	0.172
r_xyhbond_nbd_refined	0.103
r_nbtor_other	0.089
r_chiral_restr	0.07
r_symmetry_hbond_refined	0.055
r_bond_refined_d	0.015
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1797
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MolProbity	model building