9NK2 | pdb_00009nk2

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		PhdC apo model 1.5A structure solved previously from our group

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	1:1 crystallization condition (100 mM Citric acid/NaOH pH 5, 20% (w/v) PEG 6K) to protein (20mM bistris pH 7.2, 200mM KCl, reconstituted with prFMN)

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.24

Symmetry
Space Group	I 2 2 2

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 EIGER2 XE CdTe 16M		2024-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.976	MAX IV	BioMAX

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	1.81	30.51	99.9	0.08	0.086	0.025	0.999	14.4	10.9		16947

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	1.81	1.85	98.7		0.741	0.804	0.3	0.846	2.3	6.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.81	29.604	16946	871	99.829	0.158	0.1561	0.1681	0.1866	0.2018	40.362

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]
0.163			-0.511		0.348

RMS Deviations
Key	Refinement Restraint Deviation
r_scbond_it	37.941
r_scbond_other	37.931
r_scangle_it	31.999
r_scangle_other	31.982
r_dihedral_angle_other_1_deg	27.278
r_lrange_it	23.998
r_lrange_other	23.998
r_dihedral_angle_6_deg	15.401
r_dihedral_angle_3_deg	13.175
r_mcangle_other	10.129

RMS Deviations
Key	Refinement Restraint Deviation
r_scbond_it	37.941
r_scbond_other	37.931
r_scangle_it	31.999
r_scangle_other	31.982
r_dihedral_angle_other_1_deg	27.278
r_lrange_it	23.998
r_lrange_other	23.998
r_dihedral_angle_6_deg	15.401
r_dihedral_angle_3_deg	13.175
r_mcangle_other	10.129
r_mcangle_it	10.094
r_mcbond_other	9.913
r_mcbond_it	9.877
r_dihedral_angle_2_deg	8.948
r_dihedral_angle_1_deg	7.255
r_angle_refined_deg	1.833
r_angle_other_deg	0.764
r_nbd_refined	0.229
r_symmetry_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.168
r_symmetry_nbd_other	0.164
r_xyhbond_nbd_refined	0.145
r_metal_ion_refined	0.132
r_symmetry_nbd_refined	0.13
r_nbd_other	0.121
r_chiral_restr	0.098
r_symmetry_nbtor_other	0.081
r_xyhbond_nbd_other	0.027
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1183
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	42

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9NK2 | pdb_00009nk2