1VMF | pdb_00001vmf

CRYSTAL STRUCTURE OF a YBJQ-LIKE FOLD PROTEIN OF UNKNOWN FUNCTION (BH3498) FROM BACILLUS HALODURANS AT 1.46 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	7.5	277	8.0% Ethylene Glycol, 10.0% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2	VAPOR DIFFUSION, SITTING DROP, NANODROP	7.5	277	0.2M NaCl, 30.0% PEG 400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.64
2.2	43.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.601	α = 90
b = 58.951	β = 90
c = 134.964	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315	flat mirror	2004-06-11	M	MAD
2	1	x-ray	100	CCD	ADSC		2004-08-27	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1
2	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97957,0.979694,1.019859	SSRL	BL11-1

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	1.46	29.48	97.9	0.059	16.5	5.6		78750			28.11

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	1.46	1.54	92		0.742	2.4	3.7	10604

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 (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	1.46	29.48	74793	3955	97.69	0.14964	0.14832	0.16	0.17483	0.18	RANDOM	19.183

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]
0.6			-0.04		-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.922
r_dihedral_angle_3_deg	12.275
r_dihedral_angle_4_deg	10.902
r_scangle_it	6.223
r_dihedral_angle_1_deg	5.902
r_scbond_it	3.95
r_mcangle_it	2.692
r_mcbond_it	1.608
r_angle_refined_deg	1.368
r_angle_other_deg	0.826
r_mcbond_other	0.435
r_symmetry_vdw_other	0.28
r_nbd_refined	0.217
r_nbd_other	0.191
r_nbtor_refined	0.176
r_symmetry_vdw_refined	0.166
r_xyhbond_nbd_refined	0.138
r_symmetry_hbond_refined	0.133
r_metal_ion_refined	0.091
r_nbtor_other	0.082
r_chiral_restr	0.08
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3225
Nucleic Acid Atoms
Solvent Atoms	417
Heterogen Atoms	36

Software

Software
Software Name	Purpose
XDS	data scaling
SCALA	data scaling
SHELX	model building
SHARP	phasing
REFMAC	refinement
XDS	data reduction
CCP4	data scaling
SHELX	phasing