9ZIR | pdb_00009zir

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7MFI

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	5	293	0.1 M trisodium citrate pH 5.0; 0.2 M sodium chloride; 32% v/v PEG 300

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.1

Symmetry
Space Group	P 1 21 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 EIGER2 X CdTe 16M		2025-08-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8856	ESRF	ID23-1

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	2.74	71	100	0.99	7.1	6.8		18816

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	2.74	2.79			0.53

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.74	71	18804	1009	99.915	0.236	0.235	0.2408	0.257	0.2621	RANDOM	54.353

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]
0.074		1.828	-1.651		1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.426
r_dihedral_angle_6_deg	13.548
r_dihedral_angle_other_3_deg	10.088
r_dihedral_angle_1_deg	6.383
r_lrange_it	5.937
r_lrange_other	5.937
r_mcangle_it	3.89
r_mcangle_other	3.889
r_scangle_it	3.569
r_scangle_other	3.569

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.426
r_dihedral_angle_6_deg	13.548
r_dihedral_angle_other_3_deg	10.088
r_dihedral_angle_1_deg	6.383
r_lrange_it	5.937
r_lrange_other	5.937
r_mcangle_it	3.89
r_mcangle_other	3.889
r_scangle_it	3.569
r_scangle_other	3.569
r_mcbond_it	2.285
r_mcbond_other	2.284
r_scbond_it	2.043
r_scbond_other	2.043
r_angle_refined_deg	1.275
r_dihedral_angle_2_deg	1.251
r_angle_other_deg	0.493
r_nbtor_refined	0.184
r_nbd_refined	0.182
r_symmetry_nbd_other	0.163
r_nbd_other	0.142
r_xyhbond_nbd_refined	0.116
r_symmetry_nbd_refined	0.09
r_symmetry_xyhbond_nbd_refined	0.086
r_symmetry_nbtor_other	0.067
r_chiral_restr	0.059
r_ncsr_local_group_2	0.047
r_ncsr_local_group_4	0.045
r_ncsr_local_group_6	0.04
r_ncsr_local_group_3	0.037
r_ncsr_local_group_1	0.035
r_ncsr_local_group_5	0.03
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5464
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	129

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.