1TLQ

Crystal structure of protein ypjQ from Bacillus subtilis, Pfam DUF64

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Experimental electron density from Selenium SAD experiment.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.75	291	26% Peg 4k, 0.1M Tris, 0.8M Lithium Chloride, pH 8.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.112	α = 90
b = 118.112	β = 90
c = 65.792	γ = 120

Symmetry
Space Group	P 64 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	100	CCD	MARRESEARCH		2004-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9A	0.98	NSLS	X9A

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	2.4	20	99.8	0.074	31.75	11.15	20050	20050

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	2.4	2.49	99.9		0.456	4.45		1998

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	Experimental electron density from Selenium SAD experiment.	2.4	20	10470	529	99.59	0.23534	0.23244	0.29466	RANDOM	44.966

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]
2.58	1.29		2.58		-3.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.527
r_scangle_it	7.926
r_scbond_it	5.288
r_mcangle_it	3.534
r_angle_refined_deg	3.232
r_mcbond_it	2.034
r_nbd_refined	0.312
r_metal_ion_refined	0.283
r_symmetry_vdw_refined	0.281
r_chiral_restr	0.238
r_symmetry_hbond_refined	0.234
r_xyhbond_nbd_refined	0.187
r_bond_refined_d	0.046
r_gen_planes_refined	0.019

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1262
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	1

Software

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