2OH7 | pdb_00002oh7

The Crystal Structure of Cypovirus Polyhedra containing the Human ZIP-kinase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OH6	PDB entry 2OH6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			300	The crystals used to determine this structure were directly purified from cells, in vivo crystallization in the cytoplasm of the cell, temperature 300K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.742	α = 90
b = 102.742	β = 90
c = 102.742	γ = 90

Symmetry
Space Group	I 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	MAR CCD 165 mm	MD2 diffractometer	2006-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.99830	SLS	X06SA

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	2.45	20	99.9	0.128	8.2	8.2	6778	6770		-3	23.4

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)
	2.45	2.54	99.4		0.348	3.7	3.5	656

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2OH6	2.45	18.8	6744	6736	644	99.88	0.122	0.122	0.112	0.13	0.221	0.22	RANDOM	17.933

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.486
r_dihedral_angle_4_deg	24.078
r_dihedral_angle_3_deg	13.976
r_dihedral_angle_1_deg	7.383
r_scangle_it	2.475
r_angle_refined_deg	1.68
r_scbond_it	1.667
r_mcangle_it	0.947
r_angle_other_deg	0.944
r_mcbond_it	0.713
r_symmetry_vdw_other	0.22
r_symmetry_hbond_refined	0.21
r_nbd_other	0.198
r_nbd_refined	0.192
r_symmetry_vdw_refined	0.188
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.16
r_mcbond_other	0.141
r_chiral_restr	0.094
r_nbtor_other	0.088
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2007
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	95

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction