2OZZ | pdb_00002ozz

Crystal structure of YhfZ from Shigella flexneri

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	291	0.2 M Ammonium sulfate, 0.1 M Sodium citrate, pH 5.6, 20 % PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.27	α = 90
b = 62.55	β = 90
c = 170.192	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	mirrors	2006-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97912	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	2.298	37.71	99.2	0.108	10.1	14.3	23138	23138

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)
	2.298	2.38	95		0.601	2.21	8.2	2186

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.298	37.71	20590	20590	2334	98.45	0.229	0.229	0.222	0.2368	0.288	0.2968	RANDOM	64.017

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]
-1.34			0.01		1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.476
r_dihedral_angle_3_deg	19.244
r_dihedral_angle_4_deg	16.773
r_dihedral_angle_1_deg	6.621
r_scangle_it	3.183
r_scbond_it	2.179
r_angle_refined_deg	1.57
r_mcangle_it	1.452
r_mcbond_it	0.991
r_symmetry_hbond_refined	0.225
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.198
r_symmetry_vdw_refined	0.195
r_chiral_restr	0.102
r_bond_refined_d	0.017
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3586
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
SOLVE	phasing
RESOLVE	phasing
PHENIX	phasing