3VSY | pdb_00003vsy

High-resolution crystal structure of wild-type KSI in the apo form at neutral pH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CPO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	AMMONIUM SULPHATE 1.4M, 2-PROPANOL 5-7%, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.563	α = 90
b = 73.353	β = 90
c = 95.549	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 210	mirrors	2011-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

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	1.5	58.18	98.2	0.058	17	6.9	41000	40264		-3

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	1.5	1.55	84		0.49	2.7	4.8	3395

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3CPO	1.5	50	41000	40065	1605	97.72	0.1523	0.1523	0.1503	0.2017	0.2135	RANDOM	26.8173

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]
2.14			-0.12		-2.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.092
r_sphericity_free	30.884
r_dihedral_angle_4_deg	16.594
r_sphericity_bonded	15.258
r_dihedral_angle_3_deg	13.795
r_dihedral_angle_1_deg	5.695
r_rigid_bond_restr	4.607
r_angle_refined_deg	1.583
r_chiral_restr	0.117
r_bond_refined_d	0.015
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1920
Nucleic Acid Atoms
Solvent Atoms	250
Heterogen Atoms	10

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling