1YBY | pdb_00001yby

Conserved hypothetical protein Cth-95 from Clostridium thermocellum

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop, vapor diffusion	7.6	291	1.5M dipotassium hydrogen phosphate, 0.1M HEPES, pH 7.6, sitting drop, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.915	α = 90
b = 55.476	β = 120.84
c = 88.462	γ = 90

Symmetry
Space Group	C 1 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 300 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.9793	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	1.85	50	97	0.083				39625

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)
	1.85	1.92	94.8		0.541

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	1.95	27.735	34080	1054	100	0.229	0.22883	0.2275	0.2354	0.2704	0.2828	thin shells	22.504

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]
-0.655		-0.311	0.467		-0.131

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.758
r_dihedral_angle_4_deg	26.603
r_dihedral_angle_3_deg	12.822
r_dihedral_angle_1_deg	6.337
r_scangle_it	3.774
r_angle_other_deg	3.764
r_scbond_it	2.439
r_scangle_other	1.742
r_mcangle_it	1.58
r_angle_refined_deg	1.408
r_mcbond_it	0.886
r_mcangle_other	0.814
r_nbd_other	0.22
r_symmetry_vdw_other	0.208
r_nbd_refined	0.188
r_symmetry_hbond_refined	0.184
r_nbtor_refined	0.171
r_symmetry_vdw_refined	0.159
r_xyhbond_nbd_refined	0.144
r_nbtor_other	0.113
r_chiral_restr	0.086
r_bond_refined_d	0.015
r_gen_planes_other	0.006
r_gen_planes_refined	0.005
r_bond_other_d
r_mcbond_other
r_scbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2726
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms	5

Software

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