9NK4 | pdb_00009nk4

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Apo wt PhdC model solved previously by our group (deposition in progress)

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	1:1 crystallization condition (0.2M ammonium acetate, 0.1M HEPES/NaOH pH 7.5, 45% v/v MPD) to buffer (20 mM BisTris pH 7.2 200 mM)

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.77

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		2024-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.689	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	1.27	30.52	98.3	0.082	0.086	0.026	0.998	15	10.3		47805

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	1.27	1.29	84.7		0.828	0.94	0.423	0.516	2.9

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	1.27	30.512	47802	1829	98.332	0.129	0.1285	0.1308	0.1492	0.1507	19.346

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]
-1.138			0.378		0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	17.576
r_lrange_other	16.774
r_dihedral_angle_6_deg	15.599
r_dihedral_angle_2_deg	11.953
r_dihedral_angle_3_deg	11.747
r_scangle_it	11.348
r_scangle_other	11.342
r_scbond_other	8.406
r_scbond_it	8.391
r_mcangle_other	7.062

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	17.576
r_lrange_other	16.774
r_dihedral_angle_6_deg	15.599
r_dihedral_angle_2_deg	11.953
r_dihedral_angle_3_deg	11.747
r_scangle_it	11.348
r_scangle_other	11.342
r_scbond_other	8.406
r_scbond_it	8.391
r_mcangle_other	7.062
r_mcangle_it	7.052
r_dihedral_angle_1_deg	6.723
r_mcbond_it	5.229
r_mcbond_other	5.226
r_rigid_bond_restr	4.49
r_angle_refined_deg	1.972
r_angle_other_deg	0.888
r_xyhbond_nbd_other	0.351
r_symmetry_nbd_refined	0.267
r_nbd_refined	0.258
r_symmetry_xyhbond_nbd_refined	0.244
r_xyhbond_nbd_refined	0.178
r_nbtor_refined	0.176
r_symmetry_nbd_other	0.174
r_nbd_other	0.168
r_chiral_restr	0.113
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.013
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	1179
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	36

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9NK4 | pdb_00009nk4