9LVZ | pdb_00009lvz

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION	5.4	293.2	The mixture of protein solution and agarose was filled into a glass capillary, and the capillary was immersed in the reservoir solution for crystallization. The composition of the reservoir solution was as follows.15%(v/v)PEG#200,0.1 M phosphate citrate pH 5.4

Crystal Properties
Matthews coefficient	Solvent content
2.28155518	46.1228981

Symmetry
Space Group	H 3 2

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	323	PIXEL	DECTRIS EIGER X 16M		2024-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.59	44.39	100	0.116	0.13	0.057	0.999	17.2	9.8		38232

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.59	1.62	100		1.076	1.198	0.521	0.667	2.7	10.1

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1WTA	1.59	44.39	38229	1927	99.961	0.146	0.1448	0.157	0.1705	0.1799	23.324

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]
0.025	0.013		0.025		-0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.634
r_dihedral_angle_3_deg	14.631
r_lrange_other	10.188
r_lrange_it	10.187
r_dihedral_angle_2_deg	7.854
r_scangle_it	7.597
r_scangle_other	7.595
r_dihedral_angle_1_deg	6.935
r_scbond_it	4.886
r_scbond_other	4.884

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.634
r_dihedral_angle_3_deg	14.631
r_lrange_other	10.188
r_lrange_it	10.187
r_dihedral_angle_2_deg	7.854
r_scangle_it	7.597
r_scangle_other	7.595
r_dihedral_angle_1_deg	6.935
r_scbond_it	4.886
r_scbond_other	4.884
r_mcangle_it	3.477
r_mcangle_other	3.476
r_mcbond_it	2.307
r_mcbond_other	2.305
r_angle_refined_deg	1.927
r_angle_other_deg	0.662
r_nbd_refined	0.236
r_symmetry_nbd_other	0.203
r_nbd_other	0.198
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.177
r_symmetry_nbd_refined	0.15
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.07
r_dihedral_angle_other_2_deg	0.042
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2142
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms	22

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