1SED | pdb_00001sed

Crystal Structure of Protein of Unknown Function YhaL from Bacillus subtilis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	298	sodium fluoride, PEG 3350, 2-methyl 2,4 pentanediol, sodium cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.52	72.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.784	α = 111.37
b = 64.55	β = 107.19
c = 64.503	γ = 107.13

Symmetry
Space Group	P 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	SBC-2	mirrors	2004-02-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.282, 0.9793	APS	19-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	2.1	29.81	98.3	0.061	8.3	4.24	43183	41848			19.5

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	2.1	2.18	97.4		0.345	3.2	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.1	29.81	43183	41114	4117	96.9	0.189	0.189	0.18	0.209	0.2	RANDOM	37.8

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]
-1.72	2.55	2.29	0.23	2.84	1.49

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	18
c_scangle_it	4.31
c_scbond_it	2.79
c_mcangle_it	2.33
c_mcbond_it	1.61
c_angle_deg	1.2
c_improper_angle_d	0.74
c_bond_d	0.01
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2761
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	178

Software

Software
Software Name	Purpose
CNS	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
autoSHARP	phasing
ARP/wARP	model building