9KP9 | pdb_00009kp9

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8ZXX

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.08 M MES-NaOH pH 6.0, 16%(w/v) PEG6000, and 0.16 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.1

Symmetry
Space Group	P 31 2 1

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 4M		2024-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.012	Photon Factory	BL-1A

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	2.13	80.11	99.5	0.146	0.159	0.06	0.993	7.8	6.7		29428			26.76

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	2.13	2.17			0.982	1.077	0.429	0.527	1.7

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	FOURIER SYNTHESIS	THROUGHOUT	2.13	80.11	27903	1495	99.39	0.16841	0.16641	0.1783	0.20557	0.2117	RANDOM	35.694

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]
-0.35	-0.18		-0.35		1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.044
r_dihedral_angle_2_deg	7.371
r_dihedral_angle_1_deg	6.374
r_long_range_B_refined	6.276
r_long_range_B_other	6.2
r_scangle_other	4.208
r_mcangle_it	2.849
r_mcangle_other	2.848
r_scbond_it	2.664
r_scbond_other	2.663

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.044
r_dihedral_angle_2_deg	7.371
r_dihedral_angle_1_deg	6.374
r_long_range_B_refined	6.276
r_long_range_B_other	6.2
r_scangle_other	4.208
r_mcangle_it	2.849
r_mcangle_other	2.848
r_scbond_it	2.664
r_scbond_other	2.663
r_mcbond_it	1.815
r_mcbond_other	1.811
r_angle_refined_deg	1.684
r_angle_other_deg	0.541
r_chiral_restr	0.077
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded