9R55 | pdb_00009r55

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	1X8B

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	20% w/v PEG 8000, 0.2 M Magnesium acetate tetrahydrate, 0.1M Sodium cacodylate, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.9

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 XE 16M		2025-03-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.953738	Diamond	I04

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	2.67	68.69	100	0.296	0.319	0.119	0.983	6.6	7.1		17269

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	2.67	2.72		100	2.579	2.772	1.01	0.244		7.4

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.67	54.322	17244	818	99.896	0.215	0.2123	0.2137	0.264	0.2639	RANDOM	52.568

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]
0.514		3.037	-0.518		-0.153

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.257
r_dihedral_angle_6_deg	14.458
r_lrange_it	11.508
r_lrange_other	11.507
r_mcangle_it	8.465
r_mcangle_other	8.463
r_scangle_it	7.746
r_scangle_other	7.744
r_dihedral_angle_1_deg	7.163
r_dihedral_angle_2_deg	6.607

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.257
r_dihedral_angle_6_deg	14.458
r_lrange_it	11.508
r_lrange_other	11.507
r_mcangle_it	8.465
r_mcangle_other	8.463
r_scangle_it	7.746
r_scangle_other	7.744
r_dihedral_angle_1_deg	7.163
r_dihedral_angle_2_deg	6.607
r_mcbond_it	5.345
r_mcbond_other	5.342
r_scbond_it	4.868
r_scbond_other	4.867
r_angle_refined_deg	1.513
r_angle_other_deg	0.541
r_nbd_other	0.245
r_symmetry_nbd_refined	0.241
r_nbd_refined	0.235
r_symmetry_nbd_other	0.218
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.182
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.068
r_symmetry_xyhbond_nbd_other	0.049
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_symmetry_xyhbond_nbd_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3939
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	84

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.