1ZVP | pdb_00001zvp

Crystal Structure of a Protein of Unknown Function VC0802 from Vibrio cholerae, Possible Transport Protein

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	45% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.257	60.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.224	α = 90
b = 99.561	β = 90
c = 163.433	γ = 90

Symmetry
Space Group	C 2 2 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	SBC-2	mirriors	2004-12-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9798	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	2.2	50	95.1	0.077	17.44	4.5		40583	2	2	21.11

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	2.2	2.28	72.2		0.72	1.28	2.9	7744

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 (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	2.2	81.65	38512	37076	1953	96.27	0.21573	0.21404	0.21	0.24643	0.25	RANDOM	45.146

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]
0.92			-0.51		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.287
r_dihedral_angle_3_deg	19.767
r_dihedral_angle_4_deg	19.433
r_dihedral_angle_1_deg	6.143
r_scangle_it	2.3
r_angle_refined_deg	1.327
r_scbond_it	1.288
r_mcangle_it	1.215
r_mcbond_it	0.656
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.287
r_dihedral_angle_3_deg	19.767
r_dihedral_angle_4_deg	19.433
r_dihedral_angle_1_deg	6.143
r_scangle_it	2.3
r_angle_refined_deg	1.327
r_scbond_it	1.288
r_mcangle_it	1.215
r_mcbond_it	0.656
r_nbtor_refined	0.299
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.203
r_symmetry_vdw_refined	0.189
r_symmetry_hbond_refined	0.147
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3868
Nucleic Acid Atoms
Solvent Atoms	322
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.