1YEM | pdb_00001yem

Conserved hypothetical protein Pfu-838710-001 from Pyrococcus furiosus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	modified microbatch	7.9	313	1.2M sodium dihydrogen phosphate, 1.2M potassium dihydrogen sulfate, 0.1M TRIS, pH 7.9, modified microbatch, temperature 313K

Crystal Properties
Matthews coefficient	Solvent content
4.05	69.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.016	α = 90
b = 97.016	β = 90
c = 127.59	γ = 120

Symmetry
Space Group	P 31 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	MARMOSAIC 225 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0600	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	2.3	40	89.2	0.065				28161

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)
	2.3	2.38	41.5		0.16

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-Factor (All)	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	SAS	THROUGHOUT	2.3	37.932	28102	1450	89.468	0.225	0.22461	0.2228	0.24	0.2578	0.27	Thin shells	44.002

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]
1.283	0.642		1.283		-1.925

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.183
r_dihedral_angle_3_deg	13.645
r_dihedral_angle_4_deg	11.053
r_dihedral_angle_1_deg	6.755
r_mcangle_it	3.417
r_scangle_it	3.141
r_mcbond_it	2.216
r_scbond_it	1.914
r_mcangle_other	1.912
r_scangle_other	1.44
r_angle_refined_deg	1.153
r_angle_other_deg	0.683
r_scbond_other	0.559
r_mcbond_other	0.422
r_symmetry_vdw_refined	0.248
r_symmetry_vdw_other	0.204
r_nbd_refined	0.201
r_nbtor_refined	0.18
r_nbd_other	0.169
r_symmetry_hbond_refined	0.134
r_xyhbond_nbd_refined	0.102
r_nbtor_other	0.079
r_chiral_restr	0.068
r_xyhbond_nbd_other	0.053
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2696
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms	8

Software

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