9WGM | pdb_00009wgm

Crystal structure of the OcuKAI2d2 protein from Orobanche cumana

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4IH4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.2 M Magnesium chloride hexahydrate, 0.1 M Bis-Tris pH 6.5, 25% v/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.799	α = 90
b = 149.799	β = 90
c = 56.854	γ = 120

Symmetry
Space Group	P 64 2 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	PIXEL	DECTRIS EIGER X 16M		2018-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.987	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.19	49.08	91.38	0.75	24.02	20		19763

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.19	2.27	71.8		0.38	0.85	15

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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	2.19	49.08	18113	1812	91.37	0.2085	0.2233	0.2266	0.2336	RANDOM	40.861

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]
0.43	0.22		0.43		-1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.132
r_dihedral_angle_1_deg	5.863
r_scangle_it	1.983
r_scangle_other	1.983
r_mcangle_it	1.884
r_mcangle_other	1.883
r_scbond_it	1.167
r_scbond_other	1.167
r_mcbond_it	1.116
r_mcbond_other	1.116
r_angle_refined_deg	0.978
r_angle_other_deg	0.378
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.183
r_nbtor_refined	0.166
r_nbd_other	0.124
r_chiral_restr	0.047
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2073
Nucleic Acid Atoms
Solvent Atoms	28
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing