3V0E | pdb_00003v0e

Crystal structure of Ciona intestinalis voltage sensor-containing phosphatase (Ci-VSP), residues 256-576(C363S)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D5R	PDB entry 1D5R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	2.1-2.3 M ammonium sulfate, 0.1 M HEPES, pH 7.0-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.849	α = 90
b = 38.605	β = 103.99
c = 89.832	γ = 90

Symmetry
Space Group	P 1 2 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	Double Crystal Si(111)	2009-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1158	ALS	8.3.1

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	1.6	90	97.7	0.07	18.1	5.8	44934	43750	2	2

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	1.6	1.65	82.2		0.672	2.4	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1D5R	1.65	87.17	41193	38746	2058	99.05	0.17829	0.1766	0.1746	0.20959	0.2074	RANDOM	32.126

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]
-1.96		-0.63	3.71		-2.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.244
r_dihedral_angle_4_deg	14.152
r_dihedral_angle_3_deg	12.588
r_dihedral_angle_1_deg	5.352
r_scangle_it	3.078
r_scbond_it	1.934
r_mcangle_it	1.799
r_angle_refined_deg	1.081
r_rigid_bond_restr	1.007
r_mcbond_it	0.993
r_chiral_restr	0.08
r_bond_refined_d	0.008
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2570
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	34

Software

Software
Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling