9IA1 | pdb_00009ia1

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NCB

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	20 % PEG 6000, 0.2 M CaCl2 and 0.1 M MES at pH = 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.3

Symmetry
Space Group	P 41 21 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 EIGER X 16M		2021-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.8153	Diamond	I03

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	1.82	50.76	99.91	0.2547	0.2603	0.05285	0.996	7.63	23.2		85027

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	1.82	1.885	99.81		2.375	2.431	0.5122	0.658	0.83	22.4

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	FREE R-VALUE	1.82	50.76	85014	4313	99.91	0.161	0.1591	0.1599	0.2045	0.2059	24.203

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]
0.78			0.78		-1.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.966
r_dihedral_angle_3_deg	12.758
r_dihedral_angle_2_deg	7.264
r_lrange_it	6.677
r_dihedral_angle_1_deg	6.196
r_lrange_other	6.151
r_scangle_it	5.034
r_scangle_other	5.034
r_scbond_it	3.545
r_scbond_other	3.545

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.966
r_dihedral_angle_3_deg	12.758
r_dihedral_angle_2_deg	7.264
r_lrange_it	6.677
r_dihedral_angle_1_deg	6.196
r_lrange_other	6.151
r_scangle_it	5.034
r_scangle_other	5.034
r_scbond_it	3.545
r_scbond_other	3.545
r_mcangle_other	3.266
r_mcangle_it	3.263
r_mcbond_it	2.415
r_mcbond_other	2.411
r_angle_refined_deg	2.068
r_angle_other_deg	0.721
r_symmetry_nbd_refined	0.269
r_xyhbond_nbd_refined	0.258
r_nbd_refined	0.237
r_symmetry_xyhbond_nbd_refined	0.211
r_nbtor_refined	0.188
r_symmetry_nbd_other	0.184
r_nbd_other	0.151
r_chiral_restr	0.11
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6218
Nucleic Acid Atoms
Solvent Atoms	1033
Heterogen Atoms	108

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.