1M3S | pdb_00001m3s

Crystal structure of YckF from Bacillus subtilis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	PEG 8000, Na cacodylate, Ca acetate, Glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.08	α = 90
b = 72.08	β = 90
c = 245.56	γ = 120

Symmetry
Space Group	P 65 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	110	CCD	CUSTOM-MADE	Sagitally focusing double crystal monochromator and vertically focusing mirror	2002-03-17	M	MAD
2	1	x-ray	110	CCD	CUSTOM-MADE	Sagitally focusing double crystal monochromator and vertically focusing mirror	2002-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9795, 0.9793, 0.9537	APS	19-ID
2	SYNCHROTRON	APS BEAMLINE 19-ID	1.0332	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.95	60	99.6	0.072	31.6		28687	28572

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.95	2.01	100		0.468	5		2457

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.95	62.02	28572	26023	1389	95.85	0.18897	0.18897	0.18708	0.22493	RANDOM	18.524

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]
0.45	0.23		0.45		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.146
r_dihedral_angle_1_deg	5.646
r_scangle_it	4.486
r_scbond_it	2.941
r_mcangle_it	1.875
r_angle_refined_deg	1.814
r_angle_other_deg	1.176
r_mcbond_it	1.129
r_symmetry_vdw_other	0.284
r_nbd_other	0.268
r_symmetry_vdw_refined	0.246
r_nbd_refined	0.244
r_symmetry_hbond_refined	0.207
r_xyhbond_nbd_refined	0.178
r_chiral_restr	0.11
r_nbtor_other	0.092
r_bond_refined_d	0.024
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2807
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
dtDisplay	data collection
HKL-2000	data reduction
CNS	refinement
d*TREK	data scaling
d*TREK	data reduction
DTDISPLAY	data reduction
HKL-2000	data scaling
CNS	phasing