3N6Q

Crystal structure of YghZ from E. coli

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	0.2M MgFormate, 0.1M MES pH 6, 7.5% PEG 20,000, 4% 1,4 butanediol, VAPOR DIFFUSION, SITTING DROP, temperature 193K, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.7	α = 90.27
b = 98.056	β = 92.97
c = 98.257	γ = 106.12

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	ADSC QUANTUM 315r	KOHZU: Double Crystal Si(111)	2007-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11587	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.8	98	96.7	0.06	0.06	12.5	3.9	294303	294303	1	1	24.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	95		0.568	0.568	2.2	3.9	42267

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2A79	1.8	94.07	1.3	277925	14824	96.2	0.17077	0.16875	0.2087	RANDOM	29.239

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]
-0.7	-0.7	0.34	-0.52	-0.22	0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.753
r_dihedral_angle_4_deg	17.152
r_dihedral_angle_3_deg	13.701
r_dihedral_angle_1_deg	6.585
r_scangle_it	5.876
r_scbond_it	3.763
r_mcangle_it	2.359
r_angle_refined_deg	1.534
r_mcbond_it	1.475
r_chiral_restr	0.137
r_bond_refined_d	0.019
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19673
Nucleic Acid Atoms
Solvent Atoms	2642
Heterogen Atoms	9

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling