1XMX | pdb_00001xmx

Crystal structure of protein VC1899 from Vibrio cholerae

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	296	HEPES, Magnesium, Formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K, temperature 23K

Crystal Properties
Matthews coefficient	Solvent content
2.5	49.647209

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.549	α = 90
b = 71.439	β = 90
c = 90.096	γ = 90

Symmetry
Space Group	P 21 21 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	CUSTOM-MADE		2004-08-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	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	2.1	50	92.5	0.139			26064	24106

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	2.18	59.3		0.739	1.358	3.8	1511

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	2.1	50	24425	22708	1217	92.97	0.17261	0.17261	0.16836	0.1733	0.25371	0.2502	RANDOM	26.606

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]
-1.19			0.49		0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.908
r_dihedral_angle_4_deg	20.589
r_dihedral_angle_3_deg	17.001
r_dihedral_angle_1_deg	6.352
r_scangle_it	3.025
r_mcangle_it	2.618
r_scbond_it	2.037
r_angle_refined_deg	1.777
r_mcbond_it	1.7
r_symmetry_vdw_refined	0.318
r_nbtor_refined	0.316
r_symmetry_hbond_refined	0.273
r_nbd_refined	0.268
r_xyhbond_nbd_refined	0.262
r_chiral_restr	0.122
r_bond_refined_d	0.019
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3036
Nucleic Acid Atoms
Solvent Atoms	396
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
HKL-3000	phasing