Experiment: 9RZ8

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9I2T

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295.15	4 M ammonium acetate, 0.1 M Bis-Trispropane, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.98	69.09

Symmetry
Space Group	I 4 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 X 16M		2024-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.953731	Diamond	I04

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	225.57	100	0.25	0.048	0.999	10.8	27.6		498887

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03			4.601	0.929

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	2	195.541	498841	24859	99.991	0.209	0.2072	0.2169	0.2437	0.2525	44.935

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]
0.03			0.03		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.715
r_dihedral_angle_3_deg	14.932
r_dihedral_angle_6_deg	14.583
r_lrange_other	8.483
r_lrange_it	8.479
r_dihedral_angle_1_deg	7.08
r_scangle_it	6.471
r_scangle_other	6.471
r_mcangle_it	6.202
r_mcangle_other	6.202

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.715
r_dihedral_angle_3_deg	14.932
r_dihedral_angle_6_deg	14.583
r_lrange_other	8.483
r_lrange_it	8.479
r_dihedral_angle_1_deg	7.08
r_scangle_it	6.471
r_scangle_other	6.471
r_mcangle_it	6.202
r_mcangle_other	6.202
r_scbond_it	4.289
r_scbond_other	4.289
r_mcbond_it	4.286
r_mcbond_other	4.286
r_dihedral_angle_other_2_deg	2.666
r_angle_refined_deg	1.742
r_angle_other_deg	0.576
r_nbd_refined	0.226
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.181
r_nbd_other	0.178
r_xyhbond_nbd_refined	0.165
r_symmetry_nbd_refined	0.148
r_symmetry_xyhbond_nbd_refined	0.141
r_symmetry_xyhbond_nbd_other	0.125
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.079
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	32568
Nucleic Acid Atoms
Solvent Atoms	1562
Heterogen Atoms	840

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.

9RZ8 | pdb_00009rz8